I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[15991]
Open Access
Abstract: Japanese encephalitis (JE) is inflammation and swelling of the brain caused by the JE virus (JEV), a mosquito-borne member of the Flavivirus family. There are around 68,000 JE cases worldwide each year, many of which result in permanent brain damage and death. There is no specific treatment for JE. Here we present the crystal structure of the JEV capsid protein, a potential drug target, at 1.98 Å, and compare it to other flavivirus capsid proteins. The JEV capsid has a helical secondary structure (α helixes 1–4) and a similar protein fold to the dengue virus (DENV), the West Nile virus (WNV), and the Zika virus (ZIKV) capsid proteins. It forms a homodimer by antiparallel pairing with another subunit (‘) through α-helix 1-1’, 2-2’, and 4-4’ interactions. This dimeric form is believed to be the building block of the nucleocapsid. The flexibility of the N-terminal α helix-1 allows the formation of closed and open conformations with possible functional importance. The basic C-terminal pairing of α4-4’ forms a coiled-coil-like structure, indicating possible nucleic acid binding functionality. However, a comparison with other nucleic acid interacting domains indicates that homodimerization would preclude binding. This is the first JEV capsid protein to be described and is an addition to the structural biology of the Flavivirus.
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Jul 2019
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[15768]
Abstract: Controlled directional transport of molecules is essential to complex natural systems, exemplified by cellular transport up to organismal circulatory systems. In contrast to these natural systems, synthetic systems that enable transport of molecules between several spatial locations on the macroscopic scale, when external stimuli are applied, remain to be explored. Here we report the transfer of a supramolecular cage with controlled directionality between three phases, based on the cage that responds reversibly in two distinct ways to different anions. Notably, circulatory phase transfer of the cage was demonstrated based on a system where the three layers of solvent are arranged within a circular track. The direction of circulation between solvent phases depended upon the order of addition of anions.
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Jul 2019
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Diamond Proposal Number(s):
[14794, 19951]
Open Access
Abstract: Self-splicing inteins are mobile genetic elements invading host genes via nested homing endonuclease (HEN) domains. All HEN domains residing within inteins are inserted at a highly conserved insertion site. A purifying selection mechanism directing the location of the HEN insertion site has not yet been identified. In this work, we solved the three-dimensional crystal structures of two inteins inserted in the cell division control protein 21 of the hyperthermophilic archaea Pyrococcus abyssi and Pyrococcus horikoshii. A comparison between the structures provides the structural basis for the thermo-stabilization mechanism of inteins that have lost the HEN domain during evolution. The presence of an entire extein domain in the intein structure from Pyrococcus horikoshii suggests the selection mechanism for the highly conserved HEN insertion point.
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Jul 2019
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[17001]
Open Access
Abstract: The sintering of bioactive glasses allows for the preparation of complex structures, such as three‐dimensional porous scaffolds. Such 3D constructs are particularly interesting for clinical applications of bioactive glasses in bone regeneration, as the scaffolds can act as a guide for in‐growing bone cells, allowing for good integration with existing and newly formed tissue while the scaffold slowly degrades. Owing to the pronounced tendency of many bioactive glasses to crystallize upon heat treatment, 3D scaffolds have not been much exploited commercially. Here, we investigate the influence of crystallization on the sintering behavior of several bioactive glasses. In a series of mixed‐alkali glasses an increased CaO/alkali metal oxide ratio improved sintering compared to Bioglass 45S5, where dense sintering was inhibited. Addition of small amounts of calcium fluoride helped to keep melting and sintering temperatures low. Unlike glass 13‐93, these new glasses crystallized during sintering but this did not prevent densification. Variation in bioactive glass particle size allowed for fine‐tuning the microporosity resulting from the sintering process.
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Jul 2019
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I03-Macromolecular Crystallography
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Daniel
Merk
,
Sridhar
Sreeramulu
,
Denis
Kudlinzki
,
Krishna
Saxena
,
Verena
Linhard
,
Santosh L.
Gande
,
Fabian
Hiller
,
Christina
Lamers
,
Ewa
Nilsson
,
Anna
Aagaard
,
Lisa
Wissler
,
Niek
Dekker
,
Krister
Bamberg
,
Manfred
Schubert-zsilavecz
,
Harald
Schwalbe
Open Access
Abstract: The bile acid-sensing transcription factor farnesoid X receptor (FXR) regulates multiple metabolic processes. Modulation of FXR is desired to overcome several metabolic pathologies but pharmacological administration of full FXR agonists has been plagued by mechanism-based side effects. We have developed a modulator that partially activates FXR in vitro and in mice. Here we report the elucidation of the molecular mechanism that drives partial FXR activation by crystallography- and NMR-based structural biology. Natural and synthetic FXR agonists stabilize formation of an extended helix α11 and the α11-α12 loop upon binding. This strengthens a network of hydrogen bonds, repositions helix α12 and enables co-activator recruitment. Partial agonism in contrast is conferred by a kink in helix α11 that destabilizes the α11-α12 loop, a critical determinant for helix α12 orientation. Thereby, the synthetic partial agonist induces conformational states, capable of recruiting both co-repressors and co-activators leading to an equilibrium of co-activator and co-repressor binding.
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Jul 2019
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I15-Extreme Conditions
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Abstract: Using synchrotron x-ray diffraction, we show that the long-accepted monoclinic structure of the “collapsed” high-pressure phases reported in seven lanthanide elements [Nd, Tb, Gd, Dy, Ho, Er, and (probably) Tm] is incorrect. In Tb, Gd, Dy, Ho, Er, and Tm we show that the collapsed phases have a 16-atom orthorhombic structure (
o
F
16
) not previously seen in the elements, whereas in Nd we show that it has an eight-atom orthorhombic structure (
o
F
8
) previously reported in several actinide elements.
o
F
16
and
o
F
8
are members of a new family of layered elemental structures, the discovery of which reveals that the high-pressure structural systematics of the lanthanides, actinides, and group-III elements (Sc and Y) are much more related than previously imagined. Electronic structure calculations of Tb, combined with quantum many-body corrections, confirm the experimental observation, and calculate that the collapsed orthorhombic phase is a ferromagnet, nearly degenerate with an antiferromagnetic state between 60 and 80 GPa. We find that the magnetic properties of Tb survive to the highest pressures obtained in our experiments (110 GPa). Further calculations of the collapsed phases of Gd and Dy, again using the correct crystal structure, show the former to be a type-A antiferromagnet, whereas the latter is ferromagnetic.
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Jul 2019
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B22-Multimode InfraRed imaging And Microspectroscopy
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Open Access
Abstract: Fourier-transform infrared (FTIR) spectroscopy is a widespread and highly sensitive analytical method for the identification and characterization of a wide range of materials via their infrared (IR) absorption bands. Until now, the potential of IR microspectroscopy and imaging for the characterization of works of art or other objects of cultural heritage significance has been only partially exploited; in particular the use of the synchrotron radiation (SR) IR microprobe to study, at the micron scale, materials of interest for archaeological and cultural heritage studies has become popular only in the past decade. One of the main requirements imposed on the studies of ancient and/or valuable materials is that the techniques applied must be non-destructive. In this scenario, SRbased FTIR methods are perfectly suitable. Moreover, IR spectroscopy and imaging are emerging techniques that combine the assets of IR in terms of molecular specificity with the unique properties of synchrotron light. SR-FTIR micro-spectroscopy offers great advantages over conventional methods because it provides a broader spectrum (down to THz) and higher spectral quality (signal/noise ratio) at the highest spatial resolution (diffraction limited). This is due to the high brilliance and collimation of SR-IR, while still being non-damaging to the investigated system. The unique SR-IR parameters are essential for the compositional analysis of the tiny, sub-millimetric samples characteristic of ancient materials, which are heterogeneous by nature, and with complex molecular distributions at extremely variable concentrations. SR-FTIR spectroscopy and imaging can be applied successfully to the characterization of organic and inorganic materials via so-called IR fingerprinting, as well as for their compositional quantification. The range of materials investigated is very broad and encompasses painting materials, stones, glasses, ceramics, coatings on metals, paper and wooden materials, canvas or other textiles, organic colourants, resins, varnishes, cosmetics, and binding media such as glues, waxes, oils, etc. SR-IR-based methods can also be used to understand the historical technologies and to identify the raw materials used to produce archaeological artefacts and art objects, and to improve stabilization, conservation and restoration practices. Selected applications of SR-FTIR methods are discussed with a special emphasis on the chemical and mineralogical characterization of ancient paintings, on the study of alteration and corrosion layers, and the separation and identification of pigments. New perspectives offered by existing facilities and new developments in IR imaging and advanced vibrational spectroscopy that may broaden the variety of archaeological and historical materials that may be studied are outlined.
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Jul 2019
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[10369]
Open Access
Abstract: Burkholderia pseudomallei is the causative agent of the tropical disease melioidosis. Its genome encodes an arsenal of virulence factors that allow it, when required, to switch from a soil dwelling bacterium to a deadly intracellular pathogen. With a high intrinsic resistance to antibiotics and the ability to overcome challenges from the host immune system, there is an increasing requirement for new antibiotics and a greater understanding into the molecular mechanisms of B. pseudomallei virulence and dormancy. The peptidoglycan remodeling enzymes, lytic transglycosylases (Ltgs) are potential targets for such new antibiotics. Ltgs cleave the glycosidic bonds within bacterial peptidoglycan allowing for the insertion of peptidoglycan precursors during cell growth and division, and cell membrane spanning structures such as flagella and secretion systems. Using bioinformatic analysis we have identified 8 putative Ltgs in B. pseudomallei K96243. We aimed to investigate one of these Ltgs, LtgG (BPSL3046) through the generation of deletion mutants and biochemical analysis. We have shown that LtgG is a key contributor to cellular morphology, division, motility and virulence in BALB/c mice. We have determined the crystal structure of LtgG and have identified various amino acids likely to be important in peptidoglycan binding and catalytic activity. Recombinant protein assays and complementation studies using LtgG containing a site directed mutation in aspartate 343, confirmed the essentiality of this amino acid in the function of LtgG.
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Jul 2019
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[15768]
Abstract: Here we describe the formation of a trigonal prismatic cage, utilizing 2-formyl-1,8-naphthyridine subcomponents to bind pairs of silver(I) ions in close proximity. This cage is the first example of a new class of subcomponent self-assembled polyhedral structures having bimetallic vertices, as opposed to the single metal centers that typically serve as structural elements within such cages. Our new cage self-assembles around a pair of anionic templates, which are shown by crystallographic and solution-phase data to bind within the central cavity of the structure. Many different anions serve as competent templates and guests. Elongated dianions, such as the strong oxidizing agent peroxysulfate, also serve to template and bind within the cavity of the prism. The principle of using subcomponents that have more than one spatially close, but nonchelating, binding site may thus allow access to other higher-order structures with multimetallic vertices.
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Jul 2019
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Diamond Proposal Number(s):
[16931, 17932]
Abstract: Studies into the cell nucleus' incorporation of gold nanoparticles (AuNPs) are often limited by ambiguities arising from conventional imaging techniques. Indeed, it is suggested that to date there is no unambiguous imaging evidence for such uptake in whole cells, particularly at the single nanoparticle level. This shortcoming in understanding exists despite the nucleus being the most important subcellular compartment in eukaryotes and gold being the most commonly used metal nanoparticle in medical applications. Here, dual‐angle X‐ray flouresence is used to show individually resolved nanoparticles within the cell nucleus, finding them to be well separated and 79% of the intranuclear population to be monodispersed. These findings have important implications for nanomedicine, illustrated here through a specific exemplar of the predicted enhancement of radiation effects arising from the observed AuNPs, finding intranuclear dose enhancements spanning nearly five orders of magnitude.
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Jul 2019
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