I07-Surface & interface diffraction
|
Diamond Proposal Number(s):
[8225, 8733]
Open Access
Abstract: Exposure to the secondary pollutant ozone in ambient air is associated with adverse health effects when inhaled. In this work we use surface pressure measurements, combined with X-ray and neutron reflection, to observe changes in a layer of lung surfactant at the air water interface when exposed to gas phase ozone. The results demonstrate that the layer reacts with ozone changing its physical characteristics. A slight loss of material, a significant thinning of the layer and increased hydration of the surfactant material is observed. The results support the hypothesis that unsaturated lipids present in lung surfactant are still susceptible to rapid reaction with ozone and the reaction changes the properties of the interfacial layer.
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Jun 2022
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I16-Materials and Magnetism
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Diamond Proposal Number(s):
[22052, 18967]
Open Access
Abstract: Understanding and controlling the transition between antiferromagnetic states having different symmetry content with respect to time-inversion and space-group operations are fundamental challenges for the design of magnetic phases with topologically nontrivial character. Here, we consider a paradigmatic antiferromagnetic oxide insulator, Ca2RuO4, with symmetrically distinct magnetic ground states and unveil a novel path to guide the transition between them. The magnetic changeover results from structural and orbital reconstruction at the transition metal site that in turn arise as a consequence of substitutional doping. By means of resonant X-ray diffraction we track the evolution of the structural, magnetic, and orbital degrees of freedom for Mn doped Ca2RuO4 to demonstrate the mechanisms which drive the antiferromagnetic transition. While our analysis focuses on a specific case of substitution, we show that any perturbation that can impact in a similar way on the crystal structure, by reconstructing the induced spin–orbital exchange, is able to drive the antiferromagnetic reorganization.
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Jun 2022
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I04-Macromolecular Crystallography
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Open Access
Abstract: Gram-negative pathogens like Burkholderia pseudomallei use trimeric autotransporter adhesins such as BpaC as key molecules in their pathogenicity. Our 1.4 Å crystal structure of the membrane proximal part of the BpaC head domain shows that the domain is exclusively made of left-handed parallel β-roll repeats. This, the largest such structure solved, has two unique features. First, the core, rather than being composed of the canonical hydrophobic Ile and Val, is made up primarily of the hydrophilic Thr and Asn, with two different solvent channels. Second, comparing BpaC to all other left-handed parallel β-roll structures showed that the position of the head domain in the protein correlates with the number and type of charged residues. In BpaC, only negatively charged residues face the solvent – in stark contrast to the primarily positive surface charge of the left-handed parallel β-roll “type” protein, YadA. We propose extending the definitions of these head domains to include the BpaC-like head domain as a separate subtype, based on its unusual sequence, position and charge. We speculate that the function of left-handed parallel β-roll structures may differ depending on their position in the structure.
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Jun 2022
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Krios I-Titan Krios I at Diamond
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Diamond Proposal Number(s):
[21004]
Open Access
Abstract: Many cryogenic electron microscopy (cryo-EM) single particle analyses are constrained by the sample preparation step upon which aggregation, dissociation, and/or preferential orientation of particles can be introduced. Here, we report how we solved these problems in the case of CDC48A, a hexameric AAA ATPase from Arabidopsis thaliana. CDC48A hexamers are well preserved under negative staining conditions but disassemble during grid freezing using the classical blotting method. Vitrification of grids using the blot-free Chameleon method preserved the integrity of particles but resulted in their strong preferential orientation. We then used a strategy where we improved in parallel the purification of CDC48A and the conditions for cryo-EM data acquisition. Indeed, we noted that images taken from thicker ice presented an even distribution of intact particles with random orientations, but resulted in a lower image resolution. Consequently, in our case, distribution, orientation, image resolution, and the integrity of particles were tightly correlated with ice thickness. By combining the more homogeneous and stable CDC48A hexamers resulting from our improved purification protocol with an iterative search across different ice thicknesses, we identified an intermediate thickness that retained sufficiently high-resolution structural information while maintaining a complete distribution of particle orientations. Our approach may provide a simple, fast, and generally applicable strategy to record data of sufficient quality under standard laboratory and microscope settings. This method may be of particular value when time and resources are limited.
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Jun 2022
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I09-Surface and Interface Structural Analysis
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You-Ron
Lin
,
Markus
Franke
,
Shayan
Parhizkar
,
Miriam
Raths
,
Victor
Wen-Zhe Yu
,
Tien-Lin
Lee
,
Serguei
Soubatch
,
Volker
Blum
,
F. Stefan
Tautz
,
Christian
Kumpf
,
Francois C.
Bocquet
Diamond Proposal Number(s):
[17737]
Abstract: In the field of van der Waals heterostructures, the twist angle between stacked two-dimensional layers has been identified to be of utmost importance for the properties of the heterostructures. In this context, we previously reported the growth of a single layer of unconventionally oriented epitaxial graphene that forms in a surfactant atmosphere [F. C. Bocquet et al., Phys. Rev. Lett. 125, 106102 (2020)]. The resulting G-
R
0
∘
layer is aligned with the SiC lattice, and hence represents an important milestone towards high-quality twisted bilayer graphene, a frequently investigated model system in this field. Here, we focus on the surface structures obtained in the same surfactant atmosphere, but at lower preparation temperatures at which a boron nitride template layer forms on SiC(0001). In a comprehensive study based on complementary experimental and theoretical techniques, we find—in contrast to the literature—that this template layer is a hexagonal
B
x
N
y
layer, but not high-quality hBN. It is aligned with the SiC lattice and gradually replaced by low-quality graphene in the
0
∘
orientation of the
B
x
N
y
template layer upon annealing.
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Jun 2022
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B18-Core EXAFS
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Diamond Proposal Number(s):
[14239]
Open Access
Abstract: Rechargeable aqueous batteries are promising devices for large-scale energy storage applications because of their low-cost, inherent safety, and environmental friendliness. Among them, aqueous ammonium-ion (NH4+) batteries (AAIB) are currently emerging owing to the fast diffusion kinetics of NH4+. Nevertheless, it is still a challenge to obtain stable AAIB with relatively high output potential, considering the instability of many electrode materials in an aqueous environment. Herein, we report a cell based on a concentrated (5.8m) aqueous (NH4)2SO4 electrolyte, ammonium copper hexacyanoferrate (N-CuHCF) as the positiveelectrode (cathode), and 3,4,9,10-Perylene-bis(dicarboximide) (PTCDI) as the negative electrode (anode). The solvation structure, electrochemical properties, as well as the electrode-electrolyte interface and interphase are systematically investigated by the combination of theoretical and experimental methods. The results indicate for a remarkable cyling performance of the low-cost rocking-chair AAIB, which offers a capacity retention of around 72% after 1000 cycles and an average output potential of around 1.0 V.
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Jun 2022
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I10-Beamline for Advanced Dichroism
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Diamond Proposal Number(s):
[19173]
Abstract: We present an investigation on the structural and magnetic properties of the interfaces of
Fe
3
O
4
/
MgO
(
001
)
and
Fe
3
O
4
/
NiO
/
MgO
(
001
)
by extracting cation-selective magneto-optical depth profiles by means of x-ray resonant magnetic reflectivity in combination with charge-transfer multiplet simulations of x-ray magnetic circular dichroism data. For
Fe
3
O
4
/
MgO
(
001
)
, the magneto-optical depth profiles at the
Fe
2
+
oct
and the
Fe
3
+
oct
resonant energies follow exactly the structural profile, while the magneto-optical depth profile at the
Fe
3
+
tet
resonance is offset by
3.2
±
1.3
Å from the interface, consistent with a
B
-site interface termination of
Fe
3
O
4
with fully intact magnetic order. In contrast, for
Fe
3
O
4
/
NiO
(
001
)
, the magneto-optical depth profiles at the
Fe
2
+
oct
and the
Ni
2
+
resonances agree with the structural profile, but the interface positions of the magneto-optical depth profiles at the
Fe
3
+
oct
and the
Fe
3
+
tet
resonances are spatially shifted by
3.3
±
1.4
and
2.7
±
0.9
Å, respectively, not consistent with a magnetically ordered stoichiometric interface. This may be related to an intermixed
(
Ni
,
Fe
)
O
layer at the interface. The dichroic depth profile at the Ni
L
3
edge might hint at uncompensated magnetic moments throughout the NiO film.
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Jun 2022
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I03-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[24948]
Open Access
Abstract: Human topoisomerase II beta (TOP2B) modulates DNA topology using energy from ATP hydrolysis. To investigate the conformational changes that occur during ATP hydrolysis, we determined the X-ray crystallographic structures of the human TOP2B ATPase domain bound to AMPPNP or ADP at 1.9 Å and 2.6 Å resolution, respectively. The GHKL domains of both structures are similar, whereas the QTK loop within the transducer domain can move for product release. As TOP2B is the clinical target of bisdioxopiperazines, we also determined the structure of a TOP2B:ADP:ICRF193 complex to 2.3 Å resolution and identified key drug-binding residues. Biochemical characterization revealed the N-terminal strap reduces the rate of ATP hydrolysis. Mutagenesis demonstrated residue E103 as essential for ATP hydrolysis in TOP2B. Our data provide fundamental insights into the tertiary structure of the human TOP2B ATPase domain and a potential regulatory mechanism for ATP hydrolysis.
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Jun 2022
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[9475, 13467]
Open Access
Abstract: AppA, the Escherichia coli periplasmic phytase of clade 2 of the histidine phosphatase (HP2) family, has been well-characterized and successfully engineered for use as an animal feed supplement. AppA is a 1D-6-phytase and highly stereospecific but transiently accumulates 1D-myo-Ins(2,3,4,5)P4 and other lower phosphorylated intermediates. If this bottleneck in liberation of orthophosphate is to be obviated through protein engineering, an explanation of its rather rigid preference for the initial site and subsequent cleavage of phytic acid is required. To help explain this behaviour, the role of the catalytic proton donor residue in determining AppA stereospecificity was investigated. Four variants were generated by site-directed mutagenesis of the active site HDT amino acid sequence motif containing the catalytic proton donor, D304. The identity and position of the prospective proton donor residue was found to strongly influence stereospecificity. While the wild-type enzyme has a strong preference for 1D-6-phytase activity, a marked reduction in stereospecificity was observed for a D304E variant, while a proton donor-less mutant (D304A) displayed exclusive 1D-1/3-phytase activity. High-resolution X-ray crystal structures of complexes of the mutants with a non-hydrolysable substrate analogue inhibitor point to a crucial role played by D304 in stereospecificity by influencing the size and polarity of specificity pockets A and B. Taken together, these results provide the first evidence for the involvement of the proton donor residue in determining the stereospecificity of HP2 phytases and prepares the ground for structure-informed engineering studies targeting the production of animal feed enzymes capable of the efficient and complete dephosphorylation of dietary phytic acid.
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Jun 2022
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I22-Small angle scattering & Diffraction
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Abstract: Purpose : To elucidate the hierarchical deformation mechanisms of human corneal collagen under controlled inflation of physiological and pathological magnitudes.
Methods : 6 human donor corneas with scleral rim were mounted onto a bespoke sealed cell, which was connected via two pressure regulators and an expansion vessel to a source of compressed nitrogen. The cell included a window transparent to X-rays and was connected to translation and rotation stages inside beamline I22 at the Diamond Light Source synchrotron, UK. Images were acquired naso-temporally across the cornea from limbus to limbus at intraocular pressures of 5.5 mmHg, 17.5 mmHg and 40 mmHg. These increments were chosen for comparison with previous static results in the literature and to mimic the normal physiological state and ocular hypertension.
Results : The inflation apparatus was able to maintain pressure to an accuracy better than 0.1 mmHg. Features corresponding to collagen fibril diameter, spacing, D-period and orientation as well as tropocollagen spacing and orientation were measured simultaneously. Preliminary analysis revealed a radial distribution of strain (manifested as a change in D-period) across the cornea, which was accentuated in the outer periphery and limbus. In general, the interfibrillar spacing in the periphery and limbus (where collagen fibrils are arranged circumferentially) was found to increase with pressure.
Conclusions : The trends in D-period strain are indicative of bulging under increased pressure, which is pronounced at the limbus and the outer periphery. This agrees with the general consensus that the outer periphery and limbus act as a buffer zone, which takes up most of the strain under changes in intraocular pressure, and thus minimises changes in focussing power of the cornea. Further in-depth analysis of this data will allow us to calculate the supramolecular twist (which gives rise to a spring-like stretch in collagen fibrils) and examine in more detail the hierarchical response of corneal collagen to changes in intraocular pressures.
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Jun 2022
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