I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[25682]
Open Access
Abstract: The crystallographic texture development during processing of dual-phase Ti alloys like Ti-6Al-4 V is of fundamental technological importance. However, measuring texture in both phases in these materials is a significant challenge because of the spatial inhomogeneity of the texture and low volume fraction of the minority β-phase at room temperature. Here we demonstrate how synchrotron X-ray diffraction can be used to overcome these difficulties and measure texture and texture variation in hot-rolled samples in a reproducible manner. The texture in hot-rolled Ti-64 was calculated from 2D synchrotron diffraction patterns obtained along different directions. The data was analysed using MAUD, which is based on Rietveld refinement of the diffracted intensities, and using a Fourier series based analysis method, that extracts intensities directly from the 2D diffraction patterns, and then uses the open-source software MTEX to fit an orientation distribution function (ODF). By comparing the results with faithful EBSD measurements, we show that the Fourier series method produces much more accurate texture measurements, especially for the minority β-phase. We also show that a minimum of 2, and preferably 3, different measurement orientations are needed to fully represent the texture. This implies that measurements of texture which rely on diffraction data from a single sample orientation, like in fast in-situ studies or spatially resolved measurements, can only provide qualitative information and must be interpreted with care.
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Mar 2023
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B07-B-Versatile Soft X-ray beamline: High Throughput
E02-JEM ARM 300CF
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Longxiang
Liu
,
Liqun
Kang
,
Arunabhiram
Chutia
,
Jianrui
Feng
,
Martyna
Michalska
,
Pilar
Ferrer
,
David
Grinter
,
Georg
Held
,
Yeshu
Tan
,
Fangjia
Zhao
,
Fei
Guo
,
David
Hopkinson
,
Christopher
Allen
,
Yanbei
Hou
,
Junwen
Gu
,
Ioannis
Papakonstantinou
,
Paul
Shearing
,
Dan
Brett
,
Ivan P.
Parkin
,
Guanjie
He
Diamond Proposal Number(s):
[29340, 32501, 30614, 29809, 32058]
Open Access
Abstract: The electrochemical synthesis of hydrogen peroxide (H2O2) via a two-electron (2e-) oxygen reduction reaction (ORR) process provides a promising alternative to replace the energy-intensive anthraquinone process. However, the development of efficient electrocatalysts is still facing lots of challenges like insufficient understanding of active sites. Herein, we develop a facile template-protected strategy to synthesize a highly active quinone-rich porous carbon catalyst (PCC) for H2O2 electrochemical production. The optimized PCC900 exhibits unprecedented activity and selectivity, of which the onset potential reaches 0.83 V vs. reversible hydrogen electrode in 0.1 M KOH and the H2O2 selectivity is over 95 % in a wide potential range. Comprehensive synchrotron-based near-edge X-ray absorption fine structure (NEXAFS) spectroscopy combined with electrocatalytic characterizations reveals the positive correlation between quinone content and 2e- ORR performance. The effectiveness of chair-form quinone groups as the most efficient active sites is highlighted by the molecule-mimic strategy and theoretical analysis.
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Mar 2023
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B18-Core EXAFS
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Jonathan
Ruiz Esquius
,
David J.
Morgan
,
Gerardo
Algara Siller
,
Diego
Gianolio
,
Matteo
Aramini
,
Leopold
Lahn
,
Olga
Kasian
,
Simon A.
Kondrat
,
Robert
Schlögl
,
Graham J.
Hutchings
,
Rosa
Arrigo
,
Simon J.
Freakley
Diamond Proposal Number(s):
[15151]
Open Access
Abstract: The oxygen evolution reaction (OER) is crucial to future energy systems based on water electrolysis. Iridium oxides are promising catalysts due to their resistance to corrosion under acidic and oxidizing conditions. Highly active iridium (oxy)hydroxides prepared using alkali metal bases transform into low activity rutile IrO2 at elevated temperatures (>350 °C) during catalyst/electrode preparation. Depending on the residual amount of alkali metals, we now show that this transformation can result in either rutile IrO2 or nano-crystalline Li-intercalated IrOx. While the transition to rutile results in poor activity, the Li-intercalated IrOx has comparative activity and improved stability when compared to the highly active amorphous material despite being treated at 500 °C. This highly active nanocrystalline form of lithium iridate could be more resistant to industrial procedures to produce PEM membranes and provide a route to stabilize the high populations of redox active sites of amorphous iridium (oxy)hydroxides.
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Mar 2023
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[25037]
Open Access
Abstract: The use of synthetic extracellular matrices (ECMs) in fundamental in vitro cell culture studies has been instrumental for investigating the interplay between cells and matrix components. To provide cells with a more native environment in vitro, it is desirable to design matrices that are biomimetic and emulate compositional and structural features of natural ECMs. Here, the supramolecular fabrication of peptide-hyaluronan (HA) hydrogels is presented as promising ECM surrogates, combining HA and rationally designed cationic amphipatic peptides [(KI)nK, lysine (K), isoleucine (I), n = 2–6] whose mechanical properties and microstructure are tunable by the peptide sequence. (KI)nK peptides adopt β-sheet configuration and self-assemble into filamentous nanostructures triggered by pH or ionic strength. The self-assembly propensity of (KI)nK peptides increases with the sequence length, forming single phase hydrogels (shorter peptides) or with phase separation (longer peptides) in presence of the anionic polyelectrolyte HA through electrostatic complexations. The gel phase formed in (KI)nK-HA complexes exhibits viscoelastic behavior and triggers the formation of human mesenchymal stem cell (MSC) spheroids which disassemble over the time. It is anticipated that these (KI)nK-HA hydrogels with tunable physical and biochemical properties offer a promising platform for in vitro applications and in stem cell therapy.
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Mar 2023
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I12-JEEP: Joint Engineering, Environmental and Processing
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Open Access
Abstract: The Mg-Zn-Ca system has previously been proposed as the most suitable biodegradable candidate for biomedical applications. In this work, a series of ribbon specimens was fabricated using a melt-spinning technique to explore the glass-forming ability of the Mg-Zn-Ca system along the concentration line of 7 at.% of calcium. A glassy state is confirmed for Mg50Zn43Ca7, Mg60Zn33Ca7, and Mg70Zn23Ca7. Those samples were characterised by standard methods to determine their mass density, hardness, elastic modulus, and crystallisation temperatures during devitrification. Their amorphous structure is described by means of pair distribution functions obtained by high-energy X-ray and neutron diffraction (HEXRD and ND) measurements performed at large-scale facilities. The contributions of pairs Mg-Mg, Mg-Zn, and Zn-Zn were identified. In addition, a transformation process from an amorphous to crystalline structure is followed in situ by HEXRD for Mg60Zn33Ca7 and Mg50Zn43Ca7. Intermetallic compounds IM1 and IM3 and hcp-Mg phase are proposed to be formed in multiple crystallisation events.
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Mar 2023
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I03-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[17212, 23269]
Open Access
Abstract: L1 is a dizinc subclass B3 metallo-β-lactamase (MBL) that hydrolyzes most β-lactam antibiotics and is a key resistance determinant in the Gram-negative pathogen Stenotrophomonas maltophilia, an important cause of nosocomial infections in immunocompromised patients. L1 is not usefully inhibited by MBL inhibitors in clinical trials, underlying the need for further studies on L1 structure and mechanism. We describe kinetic studies and crystal structures of L1 in complex with hydrolyzed β-lactams from the penam (mecillinam), cephem (cefoxitin/cefmetazole) and carbapenem (tebipenem, doripenem and panipenem) classes. Despite differences in their structures, all the β-lactam-derived products hydrogen bond to Tyr33, Ser221 and Ser225 and are stabilized by interactions with a conserved hydrophobic pocket. The carbapenem products were modelled as Δ1-imines, with (2S)-stereochemistry. Their binding mode is determined by the presence of a 1β-methyl substituent: the Zn-bridging hydroxide either interacts with the C-6 hydroxyethyl group (1β-hydrogen-containing carbapenems), or is displaced by the C-6 carboxylate (1β-methyl-containing carbapenems). Unexpectedly, the mecillinam product is a rearranged N-formyl amide rather than penicilloic acid, with the N-formyl oxygen interacting with the Zn-bridging hydroxide. NMR studies imply mecillinam rearrangement can occur non-enzymatically in solution. Cephem-derived imine products are bound with (3R)-stereochemistry and retain their 3’ leaving groups, likely representing stable endpoints, rather than intermediates, in MBL-catalyzed hydrolysis. Our structures show preferential complex formation by carbapenem- and cephem-derived species protonated on the equivalent (β) faces, and so identify interactions that stabilize diverse hydrolyzed antibiotics. These results may be exploited in developing antibiotics, and β-lactamase inhibitors, that form long-lasting complexes with dizinc MBLs.
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Mar 2023
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I03-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Tamar
Skaist Mehlmam
,
Justin T.
Biel
,
Syeda Maryam
Azeem
,
Elliot R.
Nelson
,
Sakib
Hossain
,
Louise
Dunnett
,
Neil G.
Paterson
,
Alice
Douangamath
,
Romain
Talon
,
Danny
Axford
,
Helen
Orins
,
Frank
Von Delft
,
Daniel A.
Keedy
Diamond Proposal Number(s):
[15751, 18340, 23570]
Open Access
Abstract: Much of our current understanding of how small-molecule ligands interact with proteins stems from X-ray crystal structures determined at cryogenic (cryo) temperature. For proteins alone, room-temperature (RT) crystallography can reveal previously hidden, biologically relevant alternate conformations. However, less is understood about how RT crystallography may impact the conformational landscapes of protein-ligand complexes. Previously, we showed that small-molecule fragments cluster in putative allosteric sites using a cryo crystallographic screen of the therapeutic target PTP1B (Keedy et al., 2018). Here, we have performed two RT crystallographic screens of PTP1B using many of the same fragments, representing the largest RT crystallographic screens of a diverse library of ligands to date, and enabling a direct interrogation of the effect of data collection temperature on protein-ligand interactions. We show that at RT, fewer ligands bind, and often more weakly – but with a variety of temperature-dependent differences, including unique binding poses, changes in solvation, new binding sites, and distinct protein allosteric conformational responses. Overall, this work suggests that the vast body of existing cryo-temperature protein-ligand structures may provide an incomplete picture, and highlights the potential of RT crystallography to help complete this picture by revealing distinct conformational modes of protein-ligand systems. Our results may inspire future use of RT crystallography to interrogate the roles of protein-ligand conformational ensembles in biological function.
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Mar 2023
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I03-Macromolecular Crystallography
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Open Access
Abstract: Microbes that have evolved to live on lignocellulosic biomass face unique challenges in the effective and efficient use of this material as food. The bacterium Shewanella sp. ANA-3 has the potential to utilize arabinan and arabinoxylan, and uptake of the monosaccharide, l-arabinose, derived from these polymers, is known to be mediated by a single ABC transporter. We demonstrate that the substrate binding protein of this system, GafASw, binds specifically to l-arabinofuranose, which is the rare furanose form of l-arabinose found in lignocellulosic biomass. The structure of GafASw was resolved to 1.7 Å and comparison to Escherichia coli YtfQ (GafAEc) revealed binding site adaptations that confer specificity for furanose over pyranose forms of monosaccharides, while selecting arabinose over another related monosaccharide, galactose. The discovery of a bacterium with a natural predilection for a sugar found abundantly in certain lignocellulosic materials suggests an intimate connection in the enzymatic release and uptake of the sugar, perhaps to prevent other microbes scavenging this nutrient before it mutarotates to l-arabinopyranose. This biological discovery also provides a clear route to engineer more efficient utilization of plant biomass components in industrial biotechnology.
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Mar 2023
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B21-High Throughput SAXS
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Markus
Meier
,
Monika
Gupta
,
Serife
Akgül
,
Matthew
Mcdougall
,
Thomas
Imhof
,
Denise
Nikodemus
,
Raphael
Reuten
,
Aniel
Moya-Torres
,
Vu
To
,
Fraser
Ferens
,
Fabian
Heide
,
Gay P.
Padilla-Meier
,
Philipp
Kukura
,
Wenming
Huang
,
Birgit
Gerisch
,
Matthias
Mörgelin
,
Kate
Poole
,
Adam
Antebi
,
Manuel
Koch
,
Jörg
Stetefeld
Open Access
Abstract: Netrin-1 is a bifunctional chemotropic guidance cue that plays key roles in diverse cellular processes including axon pathfinding, cell migration, adhesion, differentiation, and survival. Here, we present a molecular understanding of netrin-1 mediated interactions with glycosaminoglycan chains of diverse heparan sulfate proteoglycans (HSPGs) and short heparin oligosaccharides. Whereas interactions with HSPGs act as platform to co-localise netrin-1 close to the cell surface, heparin oligosaccharides have a significant impact on the highly dynamic behaviour of netrin-1. Remarkably, the monomer-dimer equilibrium of netrin-1 in solution is abolished in the presence of heparin oligosaccharides and replaced with highly hierarchical and distinct super assemblies leading to unique, yet unknown netrin-1 filament formation. In our integrated approach we provide a molecular mechanism for the filament assembly which opens fresh paths towards a molecular understanding of netrin-1 functions.
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Mar 2023
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William
Mccorkindale
,
Kadi L.
Saar
,
Daren
Fearon
,
Melissa
Boby
,
Haim
Barr
,
Amir
Ben-Shmuel
,
Nir
London
,
Frank
Von Delft
,
John D.
Chodera
,
Alpha. A.
Lee
,
The
Covid Moonshot Consortium
Open Access
Abstract: A common challenge in drug design pertains to finding chemical modifications to a ligand that increases its affinity to the target protein. An underutilized advance is the increase in structural biology throughput, which has progressed from an artisanal endeavor to a monthly throughput of hundreds of different ligands against a protein in modern synchrotrons. However, the missing piece is a framework that turns high-throughput crystallography data into predictive models for ligand design. Here, we designed a simple machine learning approach that predicts protein–ligand affinity from experimental structures of diverse ligands against a single protein paired with biochemical measurements. Our key insight is using physics-based energy descriptors to represent protein–ligand complexes and a learning-to-rank approach that infers the relevant differences between binding modes. We ran a high-throughput crystallography campaign against the SARS-CoV-2 main protease (MPro), obtaining parallel measurements of over 200 protein–ligand complexes and their binding activities. This allows us to design one-step library syntheses which improved the potency of two distinct micromolar hits by over 10-fold, arriving at a noncovalent and nonpeptidomimetic inhibitor with 120 nM antiviral efficacy. Crucially, our approach successfully extends ligands to unexplored regions of the binding pocket, executing large and fruitful moves in chemical space with simple chemistry.
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Mar 2023
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