I12-JEEP: Joint Engineering, Environmental and Processing
|
W. U.
Mirihanage
,
J. D.
Robson
,
S.
Mishra
,
P.
Hidalgo-manrique
,
J.
Quinta Da Fonseca
,
C. S.
Daniel
,
P. B.
Prangnell
,
S.
Michalik
,
O. V.
Magdysyuk
,
T.
Connolley
,
M.
Drakopoulos
Diamond Proposal Number(s):
[13828]
Open Access
Abstract: An improved understanding of the phenomenon of dynamic precipitation is important to accurately model and simulate many industrial manufacturing processes with high strength Al-alloys. Dynamic ageing in 7xxx Al-alloys can occur as a result of both the strain and heat. Small angle X-ray scattering (SAXS) is an advanced technique that allows the precipitation processes to be studied in situ, but to date this has only been possible at lower than industrially relevant strain rates (e.g. < 10−3). In this contribution, we demonstrate the potential of in-situ SAXS studies of metallic alloys at higher strain rates (10−2) than previously, using a high energy synchrotron X-ray. The time resolved SAXS information has been used to evaluate dynamic precipitate evolution models and has demonstrated that at high strain rates a new regime must be considered which includes the more significant effect of vacancy annihilation, leading to a clear strain rate, rather than just strain, kinetic dependence.
|
Dec 2020
|
|
I03-Macromolecular Crystallography
|
Diamond Proposal Number(s):
[17773]
Open Access
Abstract: Tripartite α-pore-forming toxins are constructed of three proteins (A, B and C) and are found in many bacterial pathogens. While structures of the B and C components from Gram-negative bacteria have been described, the structure of the A component of a Gram-negative α-pore-forming toxin has so far proved elusive. SmhA, the A component from the opportunistic human pathogen Serratia marcescens, has been cloned, overexpressed and purified. Crystals were grown of selenomethionine-derivatized protein and anomalous data were collected. Phases were calculated and an initial electron-density map was produced.
|
Dec 2020
|
|
I04-Macromolecular Crystallography
|
David T.
Davies
,
Simon
Leiris
,
Magdalena
Zalacain
,
Nicolas
Sprynski
,
Jérôme
Castandet
,
Justine
Bousquet
,
Clarisse
Lozano
,
Agustina
Llanos
,
Laethitia
Alibaud
,
Srinivas
Vasa
,
Ramesh
Pattipati
,
Ravindar
Valige
,
Bhaskar
Kummari
,
Srinivasu
Pothukanuri
,
Cyntia
De Piano
,
Ian
Morrissey
,
Kirsty
Holden
,
Peter
Warn
,
Francesca
Marcoccia
,
Manuela
Benvenuti
,
Cecilia
Pozzi
,
Giusy
Tassone
,
Stefano
Mangani
,
Jean-denis
Docquier
,
David
Pallin
,
Richard
Elliot
,
Marc
Lemonnier
,
Martin
Everett
Diamond Proposal Number(s):
[21741]
Abstract: The diazabicyclooctanes (DBOs) are a class of serine β-lactamase (SBL) inhibitors that use a strained urea moiety as the warhead to react with the active serine residue in the active site of SBLs. The first in-class drug, avibactam, as well as several other recently approved DBOs (e.g., relebactam) or those in clinical development (e.g., nacubactam and zidebactam) potentiate activity of β-lactam antibiotics, to various extents, against carbapenem-resistant Enterobacterales (CRE) carrying class A, C, and D SBLs; however, none of these are able to rescue the activity of β-lactam antibiotics against carbapenem-resistant Acinetobacter baumannii (CRAB), a WHO “critical priority pathogen” producing class D OXA-type SBLs. Herein, we describe the chemical optimization and resulting structure–activity relationship, leading to the discovery of a novel DBO, ANT3310, which uniquely has a fluorine atom replacing the carboxamide and stands apart from the current DBOs in restoring carbapenem activity against OXA-CRAB as well as SBL-carrying CRE pathogens.
|
Dec 2020
|
|
I20-Scanning-X-ray spectroscopy (XAS/XES)
|
Open Access
Abstract: The heterogeneously catalyzed oxidation of bioethanol offers a promising route to bio-based acetic acid. Here, we assess an alternative method to support gold nanoparticles, which aims to improve selectivity to acetic acid through minimizing over-oxidation to carbon dioxide. The most promising support system is 5 wt % titanium on silica, which combines the high surface area of silica with the stabilizing effect of titania on the gold particles. Compared to gold–silica systems, which require a complex synthesis method, small quantities of titanium promoted the formation of gold nanoparticles during a simple deposition–precipitation. Characterization of the catalyst with X-ray absorption spectroscopy shows that titanium is highly dispersed in the form of small, possibly dimeric, titanium(IV) structures, which are isolated and stabilize gold nanoparticles, possibly minimizing sintering effects during synthesis. The size of the gold particles depends on the pre-treatment of the titanium–silica support before gold deposition, with larger titanium structures hosting larger gold particles. Acetic acid yield over the titanium–silica-supported gold systems improved by about 1.6 times, compared to pure titania-supported gold. The high activity of those catalysts suggests that bulk, crystalline titania is not required for the reaction, encouraging the use of mixed supports to combine their benefits. Those support systems, besides improving selectivity, offer high surface area and a low-cost filler material, which brings ethanol oxidation one step further to the industry. Additionally, the low loading of titanium permits studying the reaction mechanisms on the gold–titanium interface with bulk characterization techniques.
|
Dec 2020
|
|
B22-Multimode InfraRed imaging And Microspectroscopy
|
James M.
Cameron
,
Justin J. A.
Conn
,
Christopher
Rinaldi
,
Alexandra
Sala
,
Paul M.
Brennan
,
Michael D.
Jenkinson
,
Helen
Caldwell
,
Gianfelice
Cinque
,
Khaja
Syed
,
Holly J.
Butler
,
Mark G.
Hegarty
,
David S.
Palmer
,
Matthew J.
Baker
Diamond Proposal Number(s):
[23417]
Open Access
Abstract: Mutations in the isocitrate dehydrogenase 1 (IDH1) gene are found in a high proportion of diffuse gliomas. The presence of the IDH1 mutation is a valuable diagnostic, prognostic and predictive biomarker for the management of patients with glial tumours. Techniques involving vibrational spectroscopy, e.g., Fourier transform infrared (FTIR) spectroscopy, have previously demonstrated analytical capabilities for cancer detection, and have the potential to contribute to diagnostics. The implementation of FTIR microspectroscopy during surgical biopsy could present a fast, label-free method for molecular genetic classification. For example, the rapid determination of IDH1 status in a patient with a glioma diagnosis could inform intra-operative decision-making between alternative surgical strategies. In this study, we utilized synchrotron-based FTIR microanalysis to probe tissue microarray sections from 79 glioma patients, and distinguished the positive class (IDH1-mutated) from the IDH1-wildtype glioma, with a sensitivity and specificity of 82.4% and 83.4%, respectively. We also examined the ability of attenuated total reflection (ATR)-FTIR spectroscopy in detecting the biomolecular events and global epigenetic and metabolic changes associated with mutations in the IDH1 enzyme, in blood serum samples collected from an additional 72 brain tumour patients. Centrifugal filtration enhanced the diagnostic ability of the classification models, with balanced accuracies up to ~69%. Identification of the molecular status from blood serum prior to biopsy could further direct some patients to alternative treatment strategies.
|
Dec 2020
|
|
I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
|
Gavin W.
Collie
,
Iacovos N.
Michaelides
,
Kevin
Embrey
,
Christopher J.
Stubbs
,
Ulf
Börjesson
,
Ian L.
Dale
,
Arjan
Snijder
,
Louise
Barlind
,
Kun
Song
,
Puneet
Khurana
,
Christopher
Phillips
,
R. Ian
Storer
Open Access
Abstract: We report here a fragment screen directed toward the c-MET kinase from which we discovered a series of inhibitors able to bind to a rare conformation of the protein in which the P-loop adopts a collapsed, or folded, arrangement. Preliminary SAR exploration led to an inhibitor (7) with nanomolar biochemical activity against c-MET and promising cell activity and kinase selectivity. These findings increase our structural understanding of the folded P-loop conformation of c-MET and provide a sound structural and chemical basis for further investigation of this underexplored yet potentially therapeutically exploitable conformational state.
|
Dec 2020
|
|
I12-JEEP: Joint Engineering, Environmental and Processing
|
Diamond Proposal Number(s):
[22178]
Abstract: Fluid release from dehydration reactions is considered to have significant effects on the strength and dynamics of tectonic faults at convergent plate boundaries. It is classically assumed that the production of fluid leads to increased pore fluid pressures that perturb a fault's stress state and thereby facilitates and enhances deformation. This important assumption has never been supported by direct microstructural observations. Here, we investigate the role of gypsum dehydration in the deformation of evaporitic rocks using synchrotron-based time-resolved X-ray computed microtomography (4D) imaging. This approach enables the documentation of coupled chemical, hydraulic and mechanical processes on the grain scale. In our experiments with deforming halite-gypsum-halite sandwiches we observe that the fluid released by dehydrating gypsum accumulates at the gypsum-halite interface before a distributed hydraulic failure of the halite layer drains the fluid. From our observations we conclude that perceivedly impermeable halite layers in evaporites are unlikely to trap overpressured fluid, e.g., in thin-skinned tectonic detachment horizons. Moreover, as the hydraulic failure is diffuse and not localized, our experiments suggest that dehydration reactions alone may not explain intermediate depth seismicity in subduction zones. Our data demonstrate the significant potential that in-situ 4D imaging has for the grain-scale investigation of fundamental tectonic processes.
|
Dec 2020
|
|
B18-Core EXAFS
|
Abstract: This work describes the transformation of Pd species under reaction conditions to control the reactivity of heterogeneous catalysts, in which the real active sites for hydrogenation differ from simple Pd sites on a carbon nanofiber. Specifically, in the presence of C2H2/C2H4/H2 reaction mixtures, a permeable amorphous hydrocarbon overlayer is formed with simultaneous insertion of carbon atoms into the Pd lattice that drives the formation of low-coordinated Pd-carbide, thus providing more reactive Pd–Csub@Clayer sites (Csub: subsurface carbon; Clayer: carbon layer on the surface). The combination of these surface and subsurface effects hinders Pd-hydride, weakens ethylene adsorption confirmed by density functional theory (DFT) calculation, and thus improves catalytic behavior for selective hydrogenation of acetylene (93% ethylene selectivity at 100% conversion) with long-term stability. In the absence of hydrogen, a denser more crystalline overlayer is formed with severely restricted permeability, resulting in significantly lower activity. Moreover, by X-ray absorption spectroscopy (XAS) and in situ X-ray diffraction (XRD), it is demonstrated that different active sites dominate this catalytic reaction depending on the choice of adsorbate and exposure temperature. This work represents an alternative and arguably a simpler manner to design more reactive catalytic sites with the characteristics of long-term stability and facile preparation, which would enable promising industrial applications.
|
Dec 2020
|
|
I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
|
Abstract: The enzyme (R)-3-hydroxybutyrate dehydrogenase (HBDH) catalyzes the enantioselective reduction of 3-oxocarboxylates to (R)-3-hydroxycarboxylates, the monomeric precursors of biodegradable polyesters. Despite its application in asymmetric reduction, which prompted several engineering attempts of this enzyme, the order of chemical events in the active site, their contributions to limit the reaction rate, and interactions between the enzyme and non-native 3-oxocarboxylates have not been explored. Here, a combination of kinetic isotope effects, protein crystallography, and quantum mechanics/molecular mechanics (QM/MM) calculations were employed to dissect the HBDH mechanism. Initial velocity patterns and primary deuterium kinetic isotope effects establish a steady-state ordered kinetic mechanism for acetoacetate reduction by a psychrophilic and a mesophilic HBDH, where hydride transfer is not rate limiting. Primary deuterium kinetic isotope effects on the reduction of 3-oxovalerate indicate that hydride transfer becomes more rate limiting with this non-native substrate. Solvent and multiple deuterium kinetic isotope effects suggest hydride and proton transfers occur in the same transition state. Crystal structures were solved for both enzymes complexed to NAD+:acetoacetate and NAD+:3-oxovalerate, illustrating the structural basis for the stereochemistry of the 3-hydroxycarboxylate products. QM/MM calculations using the crystal structures as a starting point predicted a higher activation energy for 3-oxovalerate reduction catalyzed by the mesophilic HBDH, in agreement with the higher reaction rate observed experimentally for the psychrophilic orthologue. Both transition states show concerted, albeit not synchronous, proton and hydride transfers to 3-oxovalerate. Setting the MM partial charges to zero results in identical reaction activation energies with both orthologues, suggesting the difference in activation energy between the reactions catalyzed by cold- and warm-adapted HBDHs arises from differential electrostatic stabilization of the transition state. Mutagenesis and phylogenetic analysis reveal the catalytic importance of His150 and Asn145 in the respective orthologues.
|
Dec 2020
|
|
I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
|
Diamond Proposal Number(s):
[11171, 15868]
Open Access
Abstract: Phosphoglucomutase 5 (PGM5) in humans is known as a structural muscle protein without enzymatic activity, but detailed understanding of its function is lacking. PGM5 belongs to the alpha-D-phosphohexomutase family and is closely related to the enzymatically active metabolic enzyme PGM1. In the Atlantic herring, Clupea harengus, PGM5 is one of the genes strongly associated with ecological adaptation to the brackish Baltic Sea. We here present the first crystal structures of PGM5, from the Atlantic and Baltic herring, differing by a single substitution Ala330Val. The structure of PGM5 is overall highly similar to structures of PGM1. The structure of the Baltic herring PGM5 in complex with the substrate glucose-1-phosphate shows conserved substrate binding and active site compared to human PGM1, but both PGM5 variants lack phosphoglucomutase activity under the tested conditions. Structure comparison and sequence analysis of PGM5 and PGM1 from fish and mammals suggest that the lacking enzymatic activity of PGM5 is related to differences in active-site loops that are important for flipping of the reaction intermediate. The Ala330Val substitution does not alter structure or biophysical properties of PGM5 but, due to its surface-exposed location, could affect interactions with protein-binding partners.
|
Dec 2020
|
|
