I03-Macromolecular Crystallography
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Andrius
Jasilionis
,
Magdalena
Plotka
,
Lei
Wang
,
Sebastian
Dorawa
,
Joanna
Lange
,
Hildegard
Watzlawick
,
Tom
Van Den Bergh
,
Bas
Vroling
,
Josef
Altenbuchner
,
Anna-Karina
Kaczorowska
,
Ehmke
Pohl
,
Tadeusz
Kaczorowski
,
Eva
Nordberg Karlsson
,
Stefanie
Freitag-Pohl
Diamond Proposal Number(s):
[18598]
Abstract: Bacteriophages encode a wide variety of cell wall disrupting enzymes that aid the viral escape in the final stages of infection. These lytic enzymes have accumulated notable interest due to their potential as novel antibacterials for infection treatment caused by multiple-drug resistant bacteria. Here, the detailed functional and structural characterization of Thermus parvatiensis prophage peptidoglycan lytic amidase AmiP, a globular Amidase_3 type lytic enzyme adapted to high temperatures is presented. The sequence and structure comparison with homologous lytic amidases reveals the key adaptation traits that ensure the activity and stability of AmiP at high temperatures. The crystal structure determined at a resolution of 1.8 Å displays a compact α/β-fold with multiple secondary structure elements omitted or shortened compared to protein structures of similar proteins. The functional characterisation of AmiP demonstrates high efficiency of catalytic activity and broad substrate specificity towards thermophilic and mesophilic bacteria strains containing Orn-type or DAP-type peptidoglycan. The here presented AmiP constitutes the most thermoactive and ultrathermostable Amidase_3 type lytic enzyme biochemically characterised with a temperature optimum at 85 °C. The extraordinary high melting temperature Tm 102.6 °C confirms fold stability up to approximately 100 °C. Furthermore, AmiP is shown to be more active over the alkaline pH range with pH optimum at pH 8.5 and tolerates NaCl up to 300 mM with the activity optimum at 25 mM NaCl. This set of beneficial characteristics suggests that AmiP can be further exploited in biotechnology.
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Jan 2023
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Open Access
Abstract: Sb- and Nb-doped Zr and Sn-umbites have been prepared using hydrothermal synthesis with both high purity and yield. All four materials display excellent removal of Cs+ cations from acidic, neutral, and basic solutions, abating at least 80% of the Cs present. This performance is retained in the presence of competing Na+ cations as well as across the pH range. The most sustained selectivity is observed in acidic media, with evidence of a minor reduction in selectivity under basic conditions. The umbites have successfully been shaped into pellets, introducing macroporosity and retaining the selective uptake of Cs in the presence of excess Na. Through thermal treatment, samples of partially Cs-exchanged umbite can be converted into dense silicate phases where radioactive Cs can be immobilized in a potential wasteform for long term storage. These findings present doped umbites as prospective materials for industrial use with selective abatement properties and capabilities for deployment followed by end of life geological disposal.
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Jan 2023
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Accelerator Physics
Optics
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Open Access
Abstract: In the Diamond Light Source storage ring, the vertical emittance is kept at 8 pm rad during operation to maintain the source brightness for the users. This is achieved by a feedback which modifies the skew quadrupole strengths, but has disadvantages such as the introduction of betatron coupling and vertical dispersion. For the proposed Diamond-II upgrade, the storage ring will have a much smaller horizontal emittance, meaning a significantly larger coupling would be required to reach the target vertical emittance, negatively affecting the off-axis injection process. To solve this problem, a feedback using the transverse multibunch feedback striplines to drive the beam at a synchrotron sideband is planned. By driving the beam resonantly in this way, the emittance can be increased without modification of the optics. This paper describes simulations of the effects of linear and non-linear optics on the excitation as well as the impact of the machine impedance for the Diamond-II storage ring.
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Jan 2023
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I02-Macromolecular Crystallography
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Diamond Proposal Number(s):
[7707]
Open Access
Abstract: The linear ubiquitin chain assembly complex synthesises linear Ub chains which constitute a binding and activation platform for components of the TNF signalling pathway. One of the components of LUBAC is the ubiquitin ligase HOIL-1 which has been shown to generate oxyester linkages on several proteins and on linear polysaccharides. We show that HOIL-1 activity requires linear tetra-Ub binding which enables HOIL-1 to mono-ubiquitylate linear Ub chains and polysaccharides. Furthermore, we describe the crystal structure of a C-terminal tandem domain construct of HOIL-1 comprising the IBR and RING2 domains. Interestingly, the structure reveals a unique bi-nuclear Zn-cluster which substitutes the second zinc finger of the canonical RING2 fold. We identify the C-terminal histidine of this bi-nuclear Zn-cluster as the catalytic base required for the ubiquitylation activity of HOIL-1. Our study suggests that the unique zinc-coordinating architecture of RING2 provides a binding platform for ubiquitylation targets.
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Jan 2023
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I13-1-Coherence
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Diamond Proposal Number(s):
[28831]
Open Access
Abstract: Diffractive optical elements such as periodic gratings are fundamental devices in X-ray imaging – a technique that medical, material science, and security scans rely upon. Fabrication of such structures with high aspect ratios at the nanoscale creates opportunities to further advance such applications, especially in terms of relaxing X-ray source coherence requirements. This is because typical grating-based X-ray phase imaging techniques (e.g., Talbot self-imaging) require a coherence length of at least one grating period and ideally longer. In this paper, the fabrication challenges in achieving high-aspect ratio nanogratings filled with gold are addressed by a combination of laser interference and nanoimprint lithography, physical vapor deposition, metal assisted chemical etching (MACE), and electroplating. This relatively simple and cost-efficient approach is unlocked by an innovative post-MACE drying step with hexamethyldisilazane, which effectively minimizes the stiction of the nanostructures. The theoretical limits of the approach are discussed and, experimentally, X-ray nanogratings with aspect ratios >40 are demonstrated. Finally, their excellent diffractive abilities are shown when exposed to a hard (12.2 keV) monochromatic X-ray beam at a synchrotron facility, and thus potential applicability in phase-based X-ray imaging.
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Jan 2023
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B21-High Throughput SAXS
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[13467]
Open Access
Abstract: Many bacteria of the genus Shewanella are facultative anaerobes able to reduce a broad range of soluble and insoluble substrates, including Fe(III) mineral oxides. Under anoxic conditions, the bacterium Shewanella oneidensis MR-1 uses a porin-cytochrome complex (Mtr) to mediate extracellular electron transfer (EET) across the outer membrane to extracellular substrates. However, it is unclear how EET prevents generating harmful reactive oxygen species (ROS) when exposed to oxic environments. The Mtr complex is expressed under anoxic and oxygen-limited conditions and contains an extracellular MtrC subunit. This has a conserved CX8C motif that inhibits aerobic growth when removed. This inhibition is caused by an increase in ROS that kills the majority of S. oneidensis cells in culture. To better understand this effect, soluble MtrC isoforms with modified CX8C were isolated. These isoforms produced increased concentrations of H2O2 in the presence of flavin mononucleotide (FMN) and greatly increased the affinity between MtrC and FMN. X-ray crystallography revealed that the molecular structure of MtrC isoforms was largely unchanged, while small-angle X-ray scattering suggested that a change in flexibility was responsible for controlling FMN binding. Together, these results reveal that FMN reduction in S. oneidensis MR-1 is controlled by the redox-active disulfide on the cytochrome surface. In the presence of oxygen, the disulfide forms, lowering the affinity for FMN and decreasing the rate of peroxide formation. This cysteine pair consequently allows the cell to respond to changes in oxygen level and survive in a rapidly transitioning environment.
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Jan 2023
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I11-High Resolution Powder Diffraction
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Abstract: Solid-state magnesium electrolytes may pave the way for novel types of rechargeable, sustainable, and cheap batteries with high volumetric and gravimetric capacities. There are, however, currently no solid-state magnesium electrolytes that fulfill the requirements for solid-state battery applications. Here, we present the synthesis, structure, and properties of six new methylamine magnesium borohydride compounds, α- and β-Mg(BH4)2·6CH3NH2, Mg(BH4)2·3CH3NH2, and α-, α′- and β-Mg(BH4)2·CH3NH2. The β-Mg(BH4)2·CH3NH2 polymorph displays a record high Mg2+ ionic conductivity of σ(Mg2+) = 1.50 × 10–4 S cm–1 at room temperature. The high Mg2+ conductivity of β-Mg(BH4)·CH3NH2 is facilitated by a one-dimensional chain-like structure interconnected by weak dihydrogen bonds and dispersion interactions, forming a migration pathway across the chains. The oxidative stability of Mg(BH4)2·CH3NH2 is ∼1.2 V vs Mg/Mg2+, and the reversible plating and stripping were confirmed by cyclic voltammetry and symmetric cell cycling, revealing high stability toward magnesium electrodes for at least 50 cycles at 60 °C.
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Jan 2023
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[17261, 20785]
Open Access
Abstract: The results are presented of a detailed combined experimental and theoretical investigation of the influence of coadsorbed electron-donating alkali atoms and the prototypical electron acceptor molecule 7,7,8,8-tetracyanoquinodimethane (TCNQ) on the Ag(100) surface. Several coadsorption phases were characterized by scanning tunneling microscopy, low-energy electron diffraction, and soft X-ray photoelectron spectroscopy. Quantitative structural data were obtained using normal-incidence X-ray standing wave (NIXSW) measurements and compared with the results of density functional theory (DFT) calculations using several different methods of dispersion correction. Generally, good agreement between theory and experiment was achieved for the quantitative structures, albeit with the prediction of the alkali atom heights being challenging for some methods. The adsorption structures depend sensitively on the interplay of molecule–metal charge transfer and long-range dispersion forces, which are controlled by the composition ratio between alkali atoms and TCNQ. The large difference in atomic size between K and Cs has negligible effects on stability, whereas increasing the ratio of K/TCNQ from 1:4 to 1:1 leads to a weakening of molecule–metal interaction strength in favor of stronger ionic bonds within the two-dimensional alkali–organic network. A strong dependence of the work function on the alkali donor–TCNQ acceptor coadsorption ratio is predicted.
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Jan 2023
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I12-JEEP: Joint Engineering, Environmental and Processing
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Open Access
Abstract: Despite being one of the most thoroughly characterised molecular crystals, hexamethylenetetramine (HMT) and its deuterated counterpart (DHMT), are still not fully understood, especially regarding anharmonic and nuclear quantum effects. In this work, an unprecedented combination of experimental techniques, including neutron and X-ray diffraction, inelastic neutron scattering, neutron transmission, and Compton scattering, all augmented ab initio by harmonic lattice dynamics calculations, was applied. The main question that motivated the presented work was the interplay between the phonon anharmonicity and isotope and nuclear quantum effects related to the zero-point energies of proton and deuteron. Signatures of the combined effects of isotopic substitution, temperature, anharmonicity and nuclear quantum effects were found in data from all experimental methods. In the case of neutron and X-ray diffraction, these signatures manifested as systematic discrepancies between the structural and atomic displacement parameters and thermal diffuse scattering obtained from harmonic lattice calculations and their experimental counterparts. To this end, an important effect was found that could not have been explained by the harmonic lattice modelling; the reverse Ubbelohde effect, i.e. the observation that deuteration decreases hydrogen bond length in HMT. In the case of neutron transmission, further discrepancies between theoretical predictions and experimental data were found at cryogenic temperatures. Finally, applying the diabatic theory of the local potential of the intermolecular hydrogen bond in HMT, it was possible to elucidate the degree of anharmonicity of the C–H···N bonds by relating it to the magnitude of the vibrational isotope effect for the C–H bond stretching observed in inelastic and neutron Compton scattering experiments. It was found that the combined nuclear quantum and anharmonic effects of the protons (deuterons) in hydrogen bonds in HMT (DHMT) manifest as systematic discrepancies between the ab initio predictions for the widths of nuclear momentum distributions and the experimental values.
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Jan 2023
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B16-Test Beamline
Optics
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Open Access
Abstract: High-speed adaptive correction of optics, based on real-time metrology feedback, has benefitted numerous scientific communities for several decades. However, it remains a major technological challenge to extend this concept into the hard x ray regime due to the necessity for active mirrors with single-digit nanometer height errors relative to a range of aspheric forms. We have developed a high-resolution, real-time, closed-loop “adaptive” optical system for synchrotron and x ray free electron laser (XFEL) applications. After calibration of the wavefront using x ray speckle scanning, the wavefront diagnostic was removed from the x ray beam path. Non-invasive control of the size and shape of the reflected x ray beam was then demonstrated by driving a piezoelectric deformable bimorph mirror at ∼1Hz
. Continuous feedback was provided by a 20 kHz direct measurement of the optical surface with picometer sensitivity using an array of interferometric sensors. This enabled a non-specialist operator to reproduce a series of pre-defined x ray wavefronts, including focused or non-Gaussian profiles, such as flattop intensity or multiple split peaks with controllable separation and relative amplitude. Such changes can be applied in any order and in rapid succession without the need for invasive wavefront diagnostic sensors that block the x ray beam for scientific usage. These innovations have the potential to profoundly change how x ray focusing elements are utilized at synchrotron radiation and XFEL sources and provide unprecedented dynamic control of photon beams to aid scientific discoveries in a wide range of disciplines.
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Jan 2023
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