I18-Microfocus Spectroscopy
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Diamond Proposal Number(s):
[17304]
Open Access
Abstract: Laser processing is a highly versatile technique for the post-synthesis treatment and modification of transition metal dichalcogenides (TMDCs). However, to date, TMDCs synthesis typically relies on large area CVD growth and lithographic post-processing for nanodevice fabrication, thus relying heavily on complex, capital intensive, vacuum-based processing environments and fabrication tools. This inflexibility necessarily restricts the development of facile, fast, very low-cost synthesis protocols. Here we show that direct, spatially selective synthesis of 2D-TMDCs devices that exhibit excellent electrical, Raman and photoluminescence properties can be realized using laser printing under ambient conditions with minimal lithographic or thermal overheads. Our simple, elegant process can be scaled via conventional laser printing approaches including spatial light modulation and digital light engines to enable mass production protocols such as roll-to-roll processing.
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Mar 2021
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[17773, 24447]
Open Access
Abstract: Tripartite members of the ClyA family of α-PFTs have recently been identified in a number of pathogenic Gram-negative bacteria, including the human pathogen Serratia marcescens. Structures of a Gram-negative A component and a tripartite α-PFT complete pore are unknown and a mechanism for pore formation is still uncertain. Here we characterise the tripartite SmhABC toxin from S. marcescens and propose a mechanism of pore assembly. We present the structure of soluble SmhA, as well as the soluble and pore forms of SmhB. We show that the β-tongue soluble structure is well conserved in the family and propose two conserved latches between the head and tail domains that are broken on the soluble to pore conformational change. Using the structures of individual components, sequence analysis and docking predictions we illustrate how the A, B and C protomers would assemble on the membrane to produce a complete tripartite α-PFT pore.
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Mar 2021
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Open Access
Abstract: Treatments for ‘superbug’ infections are the focus for innovative research, as drug resistance threatens human health and medical practices globally. In particular, Acinetobacter baumannii (Ab) infections are repeatedly reported as difficult to treat due to increasing antibiotic resistance. Therefore, there is increasing need to identify novel targets in the development of different antimicrobials. Of particular interest is fatty acid synthesis, vital for the formation of phospholipids, lipopolysaccharides/lipooligosaccharides, and lipoproteins of Gram-negative envelopes. The bacterial type II fatty acid synthesis (FASII) pathway is an attractive target for the development of inhibitors and is particularly favourable due to the differences from mammalian type I fatty acid synthesis. Discrete enzymes in this pathway include two reductase enzymes: 3-oxoacyl-acyl carrier protein (ACP) reductase (FabG) and enoyl-ACP reductase (FabI). Here, we investigate annotated FabG homologs, finding a low-molecular weight 3-oxoacyl-ACP reductase, as the most likely FASII FabG candidate, and high-molecular weight 3-oxoacyl-ACP reductase (HMwFabG), showing differences in structure and coenzyme preference. To date, this is the second bacterial high-molecular weight FabG structurally characterized, following FabG4 from Mycobacterium. We show that ΔAbHMwfabG is impaired for growth in nutrient rich media and pellicle formation. We also modelled a third 3-oxoacyl-ACP reductase, which we annotated as AbSDR. Despite containing residues for catalysis and the ACP coordinating motif, biochemical analyses showed limited activity against an acetoacetyl-CoA substrate in vitro. Inhibitors designed to target FabG proteins and thus prevent fatty acid synthesis may provide a platform for use against multidrug-resistant pathogens including A. baumannii.
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Mar 2021
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[15832]
Open Access
Abstract: The beneficial effects of Cyclooxygenases (COX) inhibitors on human health have been known for thousands of years. Nevertheless, COXs, particularly COX-1, have been linked to a plethora of human diseases such as cancer, heart failure, neurological and neurodegenerative diseases only recently. COXs catalyze the first step in the biosynthesis of prostaglandins (PGs) and are among the most important mediators of inflammation. All published structural work on COX-1 deals with the ovine isoenzyme, which is easier to produce in milligram-quantities than the human enzyme and crystallizes readily. Here, we report the long-sought structure of the human cyclooxygenase-1 (hCOX-1) that we refined to an R/Rfree of 20.82/26.37, at 3.36 Å resolution. hCOX-1 structure provides a detailed picture of the enzyme active site and the residues crucial for inhibitor/substrate binding and catalytic activity. We compared hCOX-1 crystal structure with the ovine COX-1 and human COX-2 structures by using metrics based on Cartesian coordinates, backbone dihedral angles, and solvent accessibility coupled with multivariate methods. Differences and similarities among structures are discussed, with emphasis on the motifs responsible for the diversification of the various enzymes (primary structure, stability, catalytic activity, and specificity). The structure of hCOX-1 represents an essential step towards the development of new and more selective COX-1 inhibitors of enhanced therapeutic potential.
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Feb 2021
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Richard B.
Gillis
,
Hodaya V.
Solomon
,
Lata
Govada
,
Neil J.
Oldham
,
Vlad
Dinu
,
Shahwar Imran
Jiwani
,
Philemon
Gyasi-antwi
,
Frank
Coffey
,
Andy
Meal
,
Paul S.
Morgan
,
Stephen E.
Harding
,
John R.
Helliwell
,
Naomi E.
Chayen
,
Gary G.
Adams
Open Access
Abstract: This study concerns glulisine, a rapid-acting insulin analogue that plays a fundamental role in diabetes management. We have applied a combination of methods namely X-ray crystallography, and biophysical characterisation to provide a detailed insight into the structure and function of glulisine. X-ray data provided structural information to a resolution of 1.26 Å. Crystals belonged to the H3 space group with hexagonal (centred trigonal) cell dimensions a = b = 82.44 and c = 33.65 Å with two molecules in the asymmetric unit. A unique position of D21Glu, not present in other fast-acting analogues, pointing inwards rather than to the outside surface was observed. This reduces interactions with neighbouring molecules thereby increasing preference of the dimer form. Sedimentation velocity/equilibrium studies revealed a trinary system of dimers and hexamers/dihexamers in dynamic equilibrium. This new information may lead to better understanding of the pharmacokinetic and pharmacodynamic behaviour of glulisine which might aid in improving formulation regarding its fast-acting role and reducing side effects of this drug.
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Jan 2021
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[21587]
Open Access
Abstract: Accurate modelling of particle shrinkage during biomass pyrolysis is key to the production of biochars with specific morphologies. Such biochars represent sustainable solutions to a variety of adsorption-dependent environmental remediation challenges. Modelling of particle shrinkage during biomass pyrolysis has heretofore been based solely on theory and ex-situ experimental data. Here we present the first in-situ phase-contrast X-ray imaging study of biomass pyrolysis. A novel reactor was developed to enable operando synchrotron radiography of fixed beds of pyrolysing biomass. Almond shell particles experienced more bulk shrinkage and less change in porosity than did walnut shell particles during pyrolysis, despite their similar composition. Alkaline pretreatment was found to reduce this difference in feedstock behaviour. Ex-situ synchrotron X-ray microtomography was performed to study the effects of pyrolysis on pore morphology. Pyrolysis led to a redistribution of pores away from particle surfaces, meaning newly formed surface area may be less accessible to adsorbates.
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Jan 2021
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I13-1-Coherence
I18-Microfocus Spectroscopy
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Peter
Martin
,
Christopher P.
Jones
,
Stuart
Bartlett
,
Konstantin
Ignatyev
,
Dave
Megson-smith
,
Yukihiko
Sato
,
Silvia
Cipiccia
,
Darren J.
Batey
,
Christoph
Rau
,
Keisuke
Sueki
,
Tatsuya
Ishii
,
Junya
Igarashi
,
Kazuhiko
Ninomiya
,
Atsushi
Shinohara
,
Alison
Rust
,
Thomas B.
Scott
Diamond Proposal Number(s):
[24769, 19881]
Open Access
Abstract: The structural form and elemental distribution of material originating from different Fukushima Daiichi Nuclear Power Plant reactors (Units 1 and 3) is hereby examined to elucidate their contrasting release dynamics and the current in-reactor conditions to influence future decommissioning challenges. Complimentary computed X-ray absorption tomography and X-ray fluorescence data show that the two suites of Si-based material sourced from the different reactor Units have contrasting internal structure and compositional distribution. The known event and condition chronology correlate with the observed internal and external structures of the particulates examined, which suggest that Unit 1 ejecta material sustained a greater degree of melting than that likely derived from reactor Unit 3. In particular, we attribute the near-spherical shape of Unit 1 ejecta and their internal voids to there being sufficient time for surface tension to round these objects before the hot (and so relatively low viscosity) silicate melt cooled to form glass. In contrast, a more complex internal form associated with the sub-mm particulates invoked to originate from Unit 3 suggest a lower peak temperature, over a longer duration. Using volcanic analogues, we consider the structural form of this material and how it relates to its environmental particulate stability and the bulk removal of residual materials from the damaged reactors. We conclude that the brittle and angular Unit 3 particulate are more susceptible to further fragmentation and particulate generation hazard than the round, higher-strength, more homogenous Unit 1 material.
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Dec 2020
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I02-Macromolecular Crystallography
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Diamond Proposal Number(s):
[12346]
Open Access
Abstract: Crystallization is the bottleneck in macromolecular crystallography; even when a protein crystallises, crystal packing often influences ligand-binding and protein–protein interaction interfaces, which are the key points of interest for functional and drug discovery studies. The human hypoxia-inducible factor prolyl hydroxylase 2 (PHD2) readily crystallises as a homotrimer, but with a sterically blocked active site. We explored strategies aimed at altering PHD2 crystal packing by protein modification and molecules that bind at its active site and elsewhere. Following the observation that, despite weak inhibition/binding in solution, succinamic acid derivatives readily enable PHD2 crystallization, we explored methods to induce crystallization without active site binding. Cyclic peptides obtained via mRNA display bind PHD2 tightly away from the active site. They efficiently enable PHD2 crystallization in different forms, both with/without substrates, apparently by promoting oligomerization involving binding to the C-terminal region. Although our work involves a specific case study, together with those of others, the results suggest that mRNA display-derived cyclic peptides may be useful in challenging protein crystallization cases.
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Dec 2020
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I08-Scanning X-ray Microscopy beamline (SXM)
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Diamond Proposal Number(s):
[20900]
Open Access
Abstract: We report on the detection of primordial organic matter within the carbonaceous chondrite Maribo that is distinct from the majority of organics found in extraterrestrial samples. We have applied high-spatial resolution techniques to obtain C-N isotopic compositions, chemical, and structural information of this material. The organic matter is depleted in 15N relative to the terrestrial value at around δ15N ~ -200‰, close to compositions in the local interstellar medium. Morphological investigations by electron microscopy revealed that the material consists of µm- to sub-µm-sized diffuse particles dispersed within the meteorite matrix. Electron energy loss and synchrotron X-ray absorption near-edge structure spectroscopies show that the carbon functional chemistry is dominated by aromatic and C=O bonding environments similar to primordial organics from other carbonaceous chondrites. The nitrogen functional chemistry is characterized by C-N double and triple bonding environments distinct from what is usually found in 15N-enriched organics from aqueously altered carbonaceous chondrites. Our investigations demonstrate that Maribo represents one of the least altered CM chondrite breccias found to date and contains primordial organic matter, probably originating in the interstellar medium.
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Nov 2020
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I15-1-X-ray Pair Distribution Function (XPDF)
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Diamond Proposal Number(s):
[18638, 23164]
Open Access
Abstract: Biogenic and synthetic hydroxyapatites are confounding materials whose properties remain uncertain, even after years of study. Pair distribution function (PDF) analysis was applied to hydroxyapatites in the 1970’s and 1980’s, but this area of research has not taken full advantage of the relatively recent advances in synchrotron facilities. Here, synchrotron X-ray PDF analysis is compared to techniques commonly used to characterise hydroxyapatite (such as wide angle X-ray scattering, Fourier-transform infrared spectroscopy and thermogravimetric analysis) for a range of biogenic and synthetic hydroxyapatites with a wide range of carbonate substitution. Contributions to the pair distribution function from collagen, carbonate and finite crystallite size were examined through principal component analysis and comparison of PDFs. Noticeable contributions from collagen were observed in biogenic PDFs when compared to synthetic PDFs (namely r < 15 Å), consistent with simulated PDFs of collagen structures. Additionally, changes in local structure were observed for PDFs of synthetic hydroxyapatites with differing carbonate content, notably in features near 4 Å, 8 Å and 19 Å. Regression models were generated to predict carbonate substitution from peak position within the PDFs.
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Nov 2020
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