I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[24948]
Open Access
Abstract: Bacteria are constantly challenged by bacteriophage (phage) infection and have developed multitudinous and varied resistance mechanisms. Bacteriophage Exclusion (BREX) systems protect from phage infection by generating methylation patterns at non-palindromic 6 bp sites in host bacterial DNA, to distinguish and block replication of non-self DNA. Type 1 BREX systems are comprised of six conserved core genes. Here, we present the first reported structure of a BREX core protein, BrxA from the phage defence island of Escherichia fergusonii ATCC 35469 plasmid pEFER, solved to 2.09 Å. BrxA is a monomeric protein in solution, with an all α-helical globular fold. Conservation of surface charges and structural homology modelling against known phage defence systems highlighted that BrxA contains two helix-turn-helix motifs, juxtaposed by 180°, positioned to bind opposite sides of a DNA major groove. BrxA was subsequently shown to bind dsDNA. This new understanding of BrxA structure, and first indication of BrxA biological activity, suggests a conserved mode of DNA-recognition has become widespread and implemented by diverse phage defence systems.
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Jun 2022
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[25166]
Open Access
Abstract: We present the synthesis of a novel binary metal oxide material: Ba7Mn4O15. The crystal structure has been investigated by high-resolution powder synchrotron X-ray diffraction in the temperature range of 100–300 K as well as by powder neutron diffraction at 10 and 80 K. This material represents an isostructural barium-substituted analogue of the layered material Sr7Mn4O15 that forms its own structural class. However, we find that Ba7Mn4O15 adopts a distinct magnetic ordering, resulting in a magnetoelectric ground state below 50 K. The likely magnetoelectric coupling mechanisms have been inferred from performing a careful symmetry-adapted refinement against the powder neutron diffraction experiments, as well as by making a comparison with the nonmagnetoelectric ground state of Sr7Mn4O15.
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Jun 2022
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E01-JEM ARM 200CF
E02-JEM ARM 300CF
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Diamond Proposal Number(s):
[29599]
Open Access
Abstract: Solar H2O2 produced by O2 reduction provides a green, efficient, and ecological alternative to the industrial anthraquinone process and H2/O2 direct-synthesis. We report efficient photocatalytic H2O2 production at a rate of 73.4 mM h–1 in the presence of a sacrificial donor on a structurally engineered catalyst, alkali metal-halide modulated poly(heptazine imide) (MX → PHI). The reported H2O2 production is nearly 150 and >4250 times higher than triazine structured pristine carbon nitride under UV–visible and visible light (≥400 nm) irradiation, respectively. Furthermore, the solar H2O2 production rate on MX → PHI is higher than most of the previously reported carbon nitride (triazine, tri-s-triazine), metal oxides, metal sulfides, and other metal–organic photocatalysts. A record high AQY of 96% at 365 nm and 21% at 450 nm was observed. We find that structural modulation by alkali metal-halides results in a highly photoactive MX → PHI catalyst which has a broader light absorption range, enhanced light absorption ability, tailored bandgap, and a tunable band edge position. Moreover, this material has a different polymeric structure, high O2 trapping ability, interlayer intercalation, as well as surface decoration of alkali metals. The specific C≡N groups and surface defects, generated by intercalated MX, were also considered as potential contributors to the separation of photoinduced electron–hole pairs, leading to enhanced photocatalytic activity. A synergy of all these factors contributes to a higher H2O2 production rate. Spectroscopic data help us to rationalize the exceptional photochemical performance and structural characteristics of MX → PHI.
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Jun 2022
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I24-Microfocus Macromolecular Crystallography
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Richard J.
Gildea
,
James
Beilsten-Edmands
,
Danny
Axford
,
Sam
Horrell
,
Pierre
Aller
,
James
Sandy
,
Juan
Sanchez-Weatherby
,
C. David
Owen
,
Petra
Lukacik
,
Claire
Strain-Damerell
,
Robin L.
Owen
,
Martin A.
Walsh
,
Graeme
Winter
Diamond Proposal Number(s):
[26986, 27088]
Open Access
Abstract: In macromolecular crystallography, radiation damage limits the amount of data that can be collected from a single crystal. It is often necessary to merge data sets from multiple crystals; for example, small-wedge data collections from micro-crystals, in situ room-temperature data collections and data collection from membrane proteins in lipidic mesophases. Whilst the indexing and integration of individual data sets may be relatively straightforward with existing software, merging multiple data sets from small wedges presents new challenges. The identification of a consensus symmetry can be problematic, particularly in the presence of a potential indexing ambiguity. Furthermore, the presence of non-isomorphous or poor-quality data sets may reduce the overall quality of the final merged data set. To facilitate and help to optimize the scaling and merging of multiple data sets, a new program, xia2.multiplex, has been developed which takes data sets individually integrated with DIALS and performs symmetry analysis, scaling and merging of multi-crystal data sets. xia2.multiplex also performs analysis of various pathologies that typically affect multi-crystal data sets, including non-isomorphism, radiation damage and preferential orientation. After the description of a number of use cases, the benefit of xia2.multiplex is demonstrated within a wider autoprocessing framework in facilitating a multi-crystal experiment collected as part of in situ room-temperature fragment-screening experiments on the SARS-CoV-2 main protease.
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Jun 2022
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I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[18598]
Open Access
Abstract: Bacterial cell division is a complex process requiring the coordination of multiple components to allow the appropriate spatial and temporal control of septum formation and cell scission. Peptidoglycan (PG) is the major structural component of the septum, and our recent studies in the human pathogen Staphylococcus aureus have revealed a complex, multistage PG architecture that develops during septation. Penicillin-binding proteins (PBPs) are essential for the final steps of PG biosynthesis; their transpeptidase activity links the peptide side chains of nascent glycan strands. PBP1 is required for cell division in S. aureus, and here, we demonstrate that it has multiple essential functions associated with its enzymatic activity and as a regulator of division. Loss of PBP1, or just its C-terminal PASTA domains, results in cessation of division at the point of septal plate formation. The PASTA domains can bind PG and thereby potentially coordinate the cell division process. The transpeptidase activity of PBP1 is also essential, but its loss leads to a strikingly different phenotype of thickened and aberrant septa, which is phenocopied by the morphological effects of adding the PBP1-specific β-lactam, meropenem. Together, these results lead to a model for septal PG synthesis where PBP1 enzyme activity is required for the characteristic architecture of the septum and PBP1 protein molecules enable the formation of the septal plate.
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Jun 2022
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Abstract: Cannabidiol (CBD), is a major non-psychoactive compound isolated from the cannabis plant and has been associated with the treatment of a range of conditions which are often related to voltage-gated sodium ion channels (VGSCs). The aim of this research was to use X-ray crystallography to provide a detailed insight into the interactions which occur between CBD and the prokaryotic VGSC NavMs. CBD was found to bind at a novel site deep within the fenestration of NavMs, near the central hydrophobic cavity (Sait et al., 2020). Binding at this site would block sodium ion translocation, thus providing a mechanistic explanation for CBD’s channel inhibitory effects, which were validated via electrophysiology experiments performed on designed mutants in collaborative studies with the Ruben lab (Simon Fraser University).In addition, modelling studies conducted suggested why the closely related psychoactive compound tetrahydrocannabinol (THC) may have different binding interactions with VGSCs. Comparisons were also made between the proposed Transient Receptor Potential Cation Subfamily V member 2 (TRPV2) channel CBD binding site and the NavMs binding site. Finally, thermal melt circular dichroism spectroscopic experiments were carried out to explore CBD interactions with NavMs, which showed CBD does not affect NavMs stability during interaction. In summary, this study provides, for the first time, an insight into the possible mechanism underlying CBD interactions with sodium channels.
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Jun 2022
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Abstract: Nitroreductases activate nitroaromatic antibiotics and cancer prodrugs to cytotoxic hydroxylamines and reduce quinones to quinols. Using steady-state and stopped-flow kinetics we show that the E. coli nitroreductase NfsA is 20-50 fold more active with NADPH than with NADH and that product release may be rate-limiting. The crystal structure of NfsA with NADP+ shows that a mobile loop forms a phosphate-binding pocket. The nicotinamide ring and nicotinamide ribose are mobile, as confirmed in molecular dynamics (MD) simulations. We present a model of NADPH bound to NfsA. Only one NADP+ is seen bound to the NfsA dimers, and MD simulations show that binding of a second NADP(H) cofactor is unfavourable, suggesting that NfsA and other members of this protein superfamily may have a half-of-sites mechanism.
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Jun 2022
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I09-Surface and Interface Structural Analysis
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Luke
Thomas
,
Theo D. C.
Hobson
,
Laurie J.
Phillips
,
Kieran J.
Cheetham
,
Neil
Tarbuck
,
Leanne A. H.
Jones
,
Matthew J.
Smiles
,
Chris H.
Don
,
Pardeep K.
Thakur
,
Mark
Isaacs
,
Huw
Shiel
,
Stephen
Campbell
,
Vincent
Barrioz
,
Vin
Dhanak
,
Tim
Veal
,
Jonathan D.
Major
,
Ken
Durose
Diamond Proposal Number(s):
[28268]
Open Access
Abstract: This paper is motivated by the potential advantages of higher doping and lower contact barriers in CdTe photovoltaic devices that may be realized by using n- type rather than the conventional p-type solar absorber layers. We present post-growth doping trials for indium in thin polycrystalline CdTe films using diffusion of indium metal and with indium chloride. Chemical concentrations of indium up to 1019 cm-3 were achieved and the films were verified as n-type by hard x-ray photoemission. Post growth chlorine treatment (or InCl3) was found to compensate the n-doping. Trial structures comprising CdS/CdTe:In verified that the doped absorber structures performed as expected both before and after chloride treatment, but it is recognized that this is not an optimum combination. Hence in order to identify how the advantages of n-type absorbers might be fully realized in future work, we also report simulations of a range of p-n junction combinations with n-CdTe, a number of which have the potential for high Voc.
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Jun 2022
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Ina
Pöhner
,
Antonio
Quotadamo
,
Joanna
Panecka-Hofman
,
Rosaria
Luciani
,
Matteo
Santucci
,
Pasquale
Linciano
,
Giacomo
Landi
,
Flavio
Di Pisa
,
Lucia
Dello Iacono
,
Cecilia
Pozzi
,
Stefano
Mangani
,
Sheraz
Gul
,
Gesa
Witt
,
Bernhard
Ellinger
,
Maria
Kuzikov
,
Nuno
Santarem
,
Anabela
Cordeiro-Da-Silva
,
Maria P.
Costi
,
Alberto
Venturelli
,
Rebecca C.
Wade
Open Access
Abstract: The optimization of compounds with multiple targets is a difficult multidimensional problem in the drug discovery cycle. Here, we present a systematic, multidisciplinary approach to the development of selective antiparasitic compounds. Computational fragment-based design of novel pteridine derivatives along with iterations of crystallographic structure determination allowed for the derivation of a structure–activity relationship for multitarget inhibition. The approach yielded compounds showing apparent picomolar inhibition of T. brucei pteridine reductase 1 (PTR1), nanomolar inhibition of L. major PTR1, and selective submicromolar inhibition of parasite dihydrofolate reductase (DHFR) versus human DHFR. Moreover, by combining design for polypharmacology with a property-based on-parasite optimization, we found three compounds that exhibited micromolar EC50 values against T. brucei brucei while retaining their target inhibition. Our results provide a basis for the further development of pteridine-based compounds, and we expect our multitarget approach to be generally applicable to the design and optimization of anti-infective agents.
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Jun 2022
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[26090]
Abstract: Solid-state inorganic magnesium batteries are considered as potential high energy storage devices for the future. Here we present a series of magnesium borohydride tetrahydrofuran (THF) composites, Mg(BH 4 ) 2 · x THF(−MgO), 0 ≤ x ≤ 3, as solid-state electrolytes for magnesium batteries. Three new monoclinic compounds were identified, Mg(BH 4 ) 2 ·2/3THF ( Cc ), α-Mg(BH 4 ) 2 ·2THF ( P2 1 /c ) and β-Mg(BH 4 ) 2 ·2THF ( C2 ), and the detailed structures of α− and β−Mg(BH 4 ) 2 ·2THF are presented. The magnesium ionic conductivity of composites formed by these compounds were several orders of magnitude higher than that of the distinct compounds, x = 0, 2/3, 2, and 3. The nanocomposite stabilized by MgO nanoparticles (~50 nm), Mg(BH 4 ) 2 ·1.5THF−MgO(75 wt%), displayed the highest Mg 2+ conductivity, σ(Mg 2+ ) ~10 -4 S cm -1 at 70 °C, a high ionic transport number of t ion = 0.99, and cyclic voltammetry revealed an oxidative stability of ~1.2 V vs. Mg/Mg 2+ . The electrolyte was stable towards magnesium electrodes, which allowed for stable Mg plating/stripping for at least 100 cycles at 55 °C with a current density of 0.1 mA cm -2 . Finally, a proof-of-concept rechargeable solid-state magnesium battery was assembled with a magnesium metal anode, a TiS 2 cathode providing a maximum discharge capacity of 94.2 mAh g -1 , which corresponds to y = 0.2 in Mg y TiS 2.
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Jun 2022
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