I04-Macromolecular Crystallography
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Abigail J.
Smith
,
Elise A.
Naudin
,
Caitlin L.
Edgell
,
Emily G.
Baker
,
Bram
Mylemans
,
Laura
Fitzpatrick
,
Andrew
Herman
,
Helen M.
Rice
,
David M.
Andrews
,
Natalie
Tigue
,
Derek N.
Woolfson
,
Nigel J.
Savery
Diamond Proposal Number(s):
[23269]
Open Access
Abstract: Synthetic biology applications would benefit from protein modules of reduced complexity that function orthogonally to cellular components. As many subcellular processes depend on peptide–protein or protein–protein interactions, de novo designed polypeptides that can bring together other proteins controllably are particularly useful. Thanks to established sequence-to-structure relationships, helical bundles provide good starting points for such designs. Typically, however, such designs are tested in vitro and function in cells is not guaranteed. Here, we describe the design, characterization, and application of de novo helical hairpins that heterodimerize to form 4-helix bundles in cells. Starting from a rationally designed homodimer, we construct a library of helical hairpins and identify complementary pairs using bimolecular fluorescence complementation in E. coli. We characterize some of the pairs using biophysics and X-ray crystallography to confirm heterodimeric 4-helix bundles. Finally, we demonstrate the function of an exemplar pair in regulating transcription in both E. coli and mammalian cells.
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May 2023
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I15-1-X-ray Pair Distribution Function (XPDF)
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Elsebeth J.
Pedersen
,
Theany
To
,
Søren S.
Sørensen
,
Rasmus
Christensen
,
Johan F. S.
Christensen
,
Lars R.
Jensen
,
Michal
Bockowski
,
Oxana V.
Magdysyuk
,
Maria
Diaz-Lopez
,
Yuanzheng
Yue
,
Morten M.
Smedskjaer
Diamond Proposal Number(s):
[30401]
Abstract: Methods to improve the fracture toughness of oxide glasses are needed since low fracture toughness is a major bottleneck for their applications. To overcome this, it is critically important to investigate the effect of both short- and medium-range structural features on fracture toughness. Recent work reported a record-high fracture toughness for a bulk lithium aluminoborate glass subjected to hot compression. Here, we further explore the structural origin of this high fracture toughness by subjecting different alkali aluminoborate glasses to hot compression. Through a combination of x-ray total scattering experiments and atomistic simulations, we find that hot compression causes significant changes to both the short- and medium-range order structure of the glasses, e.g., increased coordination numbers (CNs) of network forming species and decreased average size of ring-type structures. To this end, we reveal positive correlations between the pressure-induced increase in fracture toughness and (i) the increase in average CN of network forming species and (ii) the area of the first sharp diffraction peak in the structure factor. Our study thus improves the understanding of which structural features benefit intrinsic toughening of oxide glasses.
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May 2023
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I11-High Resolution Powder Diffraction
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Aizhamal
Subanbekova
,
Varvara I.
Nikolayenko
,
Andrey A.
Bezrukov
,
Debobroto
Sensharma
,
Naveen
Kumar
,
Daniel J.
O'Hearn
,
Volodymyr
Bon
,
Shi-Qiang
Wang
,
Kyriaki
Koupepidou
,
Shaza
Darwish
,
Stefan
Kaskel
,
Michael J.
Zaworotko
Diamond Proposal Number(s):
[30456]
Open Access
Abstract: In this work, we report the synthesis, structural characterisation and sorption properties of an 8-fold interpenetrated diamondoid (dia) metal–organic framework (MOF) that is sustained by a new extended linker ligand, [Cd(Imibz)2], X-dia-2-Cd, HImibz or 2 = 4-((4-(1H-imidazol-1-yl)phenylimino)methyl)benzoic acid. X-dia-2-Cd was found to exhibit reversible single-crystal-to-single-crystal (SC–SC) transformations between four distinct phases: an as-synthesised (from N,N-dimethylformamide) wide-pore phase, X-dia-2-Cd-α; a narrow-pore phase, X-dia-2-Cd-β, formed upon exposure to water; a narrow-pore phase obtained by activation, X-dia-2-Cd-γ; a medium-pore CO2-loaded phase X-dia-2-Cd-δ. While the space group remained constant in the four phases, the cell volumes and calculated void space ranged from 4988.7 Å3 and 47% (X-dia-2-Cd-α), respectively, to 3200.8 Å3 and 9.1% (X-dia-2-Cd-γ), respectively. X-dia-2-Cd-γ also exhibited a water vapour-induced structural transformation to the water-loaded X-dia-2-Cd-β phase, resulting in an S-shaped sorption isotherm. The inflection point occurred at 18% RH with negligible hysteresis on the desorption profile. Water vapour temperature-humidity swing cycling (60% RH, 300 K to 0% RH, 333 K) indicated hydrolytic stability of X-dia-2-Cd and working capacity was retained after 128 cycles of sorbent regeneration. CO2 (at 195 K) was also observed to induce a structural transformation in X-dia-2-Cd-γ and in situ PXRD studies at 1 bar of CO2, 195 K revealed the formation of X-dia-2-Cd-δ, which exhibited 31% larger unit cell volume than X-dia-2-Cd-γ.
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May 2023
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B18-Core EXAFS
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Open Access
Abstract: The Fischer–Tropsch (FT) synthesis is traditionally associated with fossil fuel consumption, but recently this technology has emerged as a keystone that enables the conversion of captured CO2 with sustainable hydrogen to energy-dense fuels and chemicals for sectors which are challenging to be electrified. Iron-based FT catalysts are promoted with alkali and transition metals to improve reducibility, activity, and selectivity. Due to their low concentration and the metastable state under reaction conditions, the exact speciation and location of these promoters remain poorly understood. We now show that the selectivity promoters such as potassium and manganese, locked into an oxidic matrix doubling as a catalyst support, surpass conventional promoting effects. La1–xKxAl1–yMnyO3−δ (x = 0 or 0.1; y = 0, 0.2, 0.6, or 1) perovskite supports yield a 60% increase in CO conversion comparable to conventional promotion but show reduced CO2 and overall C1 selectivity. The presented approach to promotion seems to decouple the enhancement of the FT and the water–gas shift reaction. We introduce a general catalyst design principle that can be extended to other key catalytic processes relying on alkali and transition metal promotion.
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May 2023
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[24948]
Open Access
Abstract: We report a chemo-biocatalytic cascade for the synthesis of substituted pyrroles, driven by the action of an irreversible, thermostable, pyridoxal 5′-phosphate (PLP)-dependent, C–C bond-forming biocatalyst (ThAOS). The ThAOS catalyzes the Claisen-like condensation between various amino acids and acyl-CoA substrates to generate a range of α-aminoketones. These products are reacted with β-keto esters in an irreversible Knorr pyrrole reaction. The determination of the 1.6 Å resolution crystal structure of the PLP-bound form of ThAOS lays the foundation for future engineering and directed evolution. This report establishes the AOS family as useful and versatile C–C bond-forming biocatalysts.
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May 2023
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I09-Surface and Interface Structural Analysis
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Diamond Proposal Number(s):
[29451]
Open Access
Abstract: Interdiffusion phenomena between adjacent materials are highly prevalent in semiconductor device architectures and can present a major reliability challenge for the industry. To fully capture these phenomena, experimental approaches must go beyond static and post-mortem studies to include in situ and in-operando setups. Here, soft and hard X-ray photoelectron spectroscopy (SXPS and HAXPES) is used to monitor diffusion in real-time across a proxy device. The device consists of a Si/SiO2/TixW1−x(300 nm)/Cu(25 nm) thin film material stack, with the TixW1−x film (x = 0.054, 0.115, 0.148) acting as a diffusion barrier between Si and Cu. The interdiffusion is monitored through the continuous collection of spectra whilst in situ annealing to 673 K. Ti within the TiW is found to be highly mobile during annealing, diffusing out of the barrier and accumulating at the Cu surface. Increasing the Ti concentration within the TixW1−x film increases the quantity of accumulated Ti, and Ti is first detected at the Cu surface at temperatures as low as 550 K. Surprisingly, at low Ti concentrations (x = 0.054), W is also mobile and diffuses alongside Ti. By monitoring the Ti 1s core level with HAXPES, the surface-accumulated Ti was observed to undergo oxidation even under ultra-high vacuum conditions, highlighting the reactivity of Ti in this system. These results provide crucial evidence for the importance of diffusion barrier composition on their efficacy during device application, delivering insights into the mechanisms underlying their effectiveness and limitations.
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May 2023
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Krios I-Titan Krios I at Diamond
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Diamond Proposal Number(s):
[19832]
Open Access
Abstract: CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes, and account for up to 95% of the viral sequences in some individuals. Crassviruses are likely to have major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the virally encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses4,5. Here we present a cryo-electron microscopy reconstruction of Bacteroides intestinalis virus ΦcrAss0016, providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms an assembly about 1 MDa in size at the end of the tail and exhibits a previously unknown fold that we designate the ‘crass fold’, that is likely to serve as a gatekeeper that controls the ejection of cargos. In addition to packing the approximately 103 kb of virus DNA, the ΦcrAss001 virion has extensive storage space for virally encoded cargo proteins in the capsid and, unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide a structural basis for understanding the mechanisms of assembly and infection of these highly abundant crassviruses.
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May 2023
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B21-High Throughput SAXS
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Biswanath
Hansda
,
Jhilam
Majumder
,
Biplab
Mondal
,
Akash
Chatterjee
,
Subhadeep
Das
,
Sourav
Kumar
,
Ratan
Gachhui
,
Valeria
Castelletto
,
Ian W.
Hamley
,
Prosenjit
Sen
,
Arindam
Banerjee
Diamond Proposal Number(s):
[29895]
Abstract: A histidine-based amphiphilic peptide (P) has been found to form an injectable transparent hydrogel in phosphate buffer solution over a pH range from 7.0 to 8.5 with an inherent antibacterial property. It also formed a hydrogel in water at pH = 6.7. The peptide self-assembles into a nanofibrillar network structure which is characterized by high-resolution transmission electron microscopy, field-emission scanning electron microscopy, atomic force microscopy, small-angle X-ray scattering, Fourier-transform infrared spectroscopy, and wide-angle powder X-ray diffraction. The hydrogel exhibits efficient antibacterial activity against both Gram-positive bacteria Staphylococcus aureus (S. aureus) and Gram-negative bacteria Escherichia coli (E. coli). The minimum inhibitory concentration of the hydrogel ranges from 20 to 100 μg/mL. The hydrogel is capable of encapsulation of the drugs naproxen (a non-steroidal anti-inflammatory drug), amoxicillin (an antibiotic), and doxorubicin, (an anticancer drug), but, selectively and sustainably, the gel releases naproxen, 84% being released in 84 h and amoxicillin was released more or less in same manner with that of the naproxen. The hydrogel is biocompatible with HEK 293T cells as well as NIH (mouse fibroblast cell line) cells and thus has potential as a potent antibacterial and drug releasing agent. Another remarkable feature of this hydrogel is its magnification property like a convex lens.
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May 2023
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I14-Hard X-ray Nanoprobe
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Lucia
Gandarias
,
Elizabeth M.
Jefremovas
,
David
Gandia
,
Lourdes
Marcano
,
Virginia
Martínez-Martínez
,
Pedro
Ramos-Cabrer
,
Daniel M.
Chevrier
,
Sergio
Valencia
,
Luis
Fernández Barquín
,
M. Luisa
Fdez-Gubieda
,
Javier
Alonso
,
Ana
García-Prieto
,
Alicia
Muela
Diamond Proposal Number(s):
[28868]
Open Access
Abstract: Magnetotactic bacteria are envisaged as potential theranostic agents. Their internal magnetic compass, chemical specificity and natural motility enable these microorganisms to behave as nanorobots, as they can be tracked and guided towards specific regions and activated to generate a therapeutic response. Here we provide additional diagnostic functionalities to magnetotactic bacteria Magnetospirillum gryphiswaldense MSR-1 while retaining their intrinsic capabilities. These additional functionalities are achieved by incorporating Tb or Gd to the bacteria by culturing them in Tb/Gd supplemented media. The incorporation of Tb provides luminescence properties, enabling potential applications of bacteria as biomarkers. The incorporation of Gd turns bacteria into dual contrast agents for magnetic resonance imaging, since Gd adds T1 contrast to the existing T2 contrast of unmodified bacteria. Given their potential clinical applications, the diagnostic ability of the modified MSR-1 has been successfully tested in vitro in two cell models, confirming their suitability as fluorescent markers (Tb-MSR-1) and dual contrast agents for MR1 (Gd-MSR-1).
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May 2023
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Insertion Devices
Magnets
Mechanical Engineering
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Abstract: The main factors that cause the X-ray beam to drift are discussed in this chapter. Issues such as movement of the source or mechanical and thermal instabilities of the main optical elements of the beamline are translated into movement of the X-ray beam at the sample, intensity drifts and nonlinearities on the energy scale, affecting the quality of the data collected. The main steps that need to be taken to prevent and/or minimize the effects of these drifts are described, and approaches such as feedback systems are presented. The polarization of the beam delivered by the different types of X-ray sources used for synchrotron-based spectroscopy experiments is also presented. The on-axis and off-axis polarizations of the bending magnet and insertion devices such as wigglers and undulators are discussed.
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May 2023
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