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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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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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
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Matthew
Mcdougall
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Thomas
Imhof
,
Denise
Nikodemus
,
Raphael
Reuten
,
Aniel
Moya-Torres
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Vu
To
,
Fraser
Ferens
,
Fabian
Heide
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Gay P.
Padilla-Meier
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Philipp
Kukura
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Wenming
Huang
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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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I20-EDE-Energy Dispersive EXAFS (EDE)
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Diamond Proposal Number(s):
[29667]
Abstract: Single-atoms on carbon-nitrogen supports are considered catalysts for a multitude of reactions. However, doubts remain whether really these species or subnanometer clusters formed under reaction conditions are the active species. In this work, we investigate the dynamics of palladium single-atoms on graphitic carbon nitride during ethylene hydrogenation and H2-D2 exchange. By employing aberration-corrected scanning transmission electron microscopy, x-ray photoelectron spectroscopy and x-ray absorption spectroscopy, we will show that palladium, originally present as single-atoms, agglomerates to clusters at 100 °C in a gas atmosphere that contains both ethylene and hydrogen. This agglomeration goes in hand with the emergence of catalytic activity in both ethylene hydrogenation and H2-D2 exchange, suggesting that clusters, rather than single-atoms, are the active species. The results presented herein highlight the potential of analytics over the course of reaction to identify the active species and provide new insights into the influence of gas atmosphere on metal speciation.
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Mar 2023
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B18-Core EXAFS
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Abstract: During my PhD research activity, I was involved in the development of smart materials with self-healing functionalities, the possibility to repair the "tissue" that constitutes the electrode, and the electrode/electrolyte interface is the first step towards improve batteries reliability. Concerning the anodic compartment, the active materials subjected to research were black phosphorus-based nanocomposite with carbon and advanced high entropy oxides with rock-salt structure. Subsequently, innovative functional cathode materials were developed for application in lithium-ion batteries that exhibits excellent cycling stability in a wide voltage range and high specific capacities. During the last year I focused on improving lithium metal battery technology, by realizing an enhanced polymer gel electrolyte by means of a Janus separator that showed excellent electrochemical performance, reduced capacity loss and the ability to intercept dendrite growth. A further improvement were Cu-based 3D current collectors as advanced anodes. They showed good capacity, life cycle of more than 300 hours and enhanced safety due to the greater surface area as well as the decrease in local current densities.
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Mar 2023
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I10-Beamline for Advanced Dichroism
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Diamond Proposal Number(s):
[16141]
Open Access
Abstract: Owing to the unique chemical and electronic properties arising from 3d-electrons, substitution with transition metal ions is one of the key routes for engineering new functionalities into materials. While this approach has been used extensively in complex metal oxide perovskites, metal halide perovskites have largely resisted facile isovalent substitution. In this work, it is demonstrated that the substitution of Co2+ into the lattice of methylammonium lead triiodide imparts magnetic behavior to the material while maintaining photovoltaic performance at low concentrations. In addition to comprehensively characterizing its magnetic properties, the Co2+ ions themselves are utilized as probes to sense the local electronic environment of Pb in the perovskite, thereby revealing the nature of their incorporation into the material. A comprehensive understanding of the effect of transition metal incorporation is provided, thereby opening the substitution gateway for developing novel functional perovskite materials and devices for future technologies.
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Mar 2023
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[20096]
Open Access
Abstract: Laser additive manufacturing is transforming several industrial sectors, especially the directed energy deposition process. A key challenge in the widespread uptake of this emerging technology is the formation of undesirable microstructural features such as pores, cracks, and large epitaxial grains. The trial and error approach to establish the relationship between process parameters and material properties is problematic due to the transient nature of the process and the number of parameters involved. In this work, the relationship between process parameters, melt pool geometry and quality of build measures, using directed energy deposition additive manufacturing for IN718, is quantified using neural networks as generalised regressors in a statistically robust manner. The data was acquired using in-situ synchrotron x-ray imaging providing unique and accurate measurements for our analysis. An analysis of the variations across repeated measurements show heteroscedastic error characteristics that are accounted for using a principled nonlinear data transformation method. The results of the analysis show that surface roughness correlates with melt pool geometry while the track height directly correlates with process parameters indicating a potential to directly control efficiency and layer thickness while independently minimising surface roughness.
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Mar 2023
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I18-Microfocus Spectroscopy
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Diamond Proposal Number(s):
[15475, 15215, 12700]
Open Access
Abstract: The agricultural soils of West Limerick, Ireland, contain very localised, extremely high natural Se concentrations that reach levels that are very toxic to grazing livestock. The Carboniferous shales that formed in anoxic deep-water marine environments are the source of the selenium, which, along with the other redox-sensitive elements of molybdenum, uranium, arsenic and vanadium, were mobilised and reprecipitated in post-glacial anoxic marshes. The result has been a history of selenosis and molybdenosis in livestock in this important dairy province. Soils collected at 10–20 cm from five different agricultural sites were analysed, and all yielded concentrations greatly in excess of the safe Se limits of 3–10 mg kg−1; the highest value recorded was 1265.8 mg kg−1 Se. The highest recorded value for Mo in these soils was 1627.5 mg kg−1, and for U, 658.8 mg kg−1. There was a positive correlation between Se, Mo U and organic matter in the soils. Analysis of non-accumulator pasture grasses (Lolium perenne (perennial ryegrass), Festuca arundinacea (tall fescue), Dactylis glomerata (cocksfoot) and Phleum pretense (timothy grass)) revealed the shoot/leaf to contain up to 78.05 mg kg−1 Se while Trifolium repens (white clover) leaves contained 296.15 mg kg−1 Se. An in situ growing experiment using the Se accumulator species Brassica oleracea revealed 971.2 mg kg−1 Se in the leaves of premier kale, which also contained 1000.4 mg kg−1 Mo. Translocation factors (TFs) were generally higher for Mo than Se across all plant species. Combined X-ray absorption near edge spectroscopy (XANES) with micro-X-ray fluorescence (μ-XRF) showed the Se was present in the soil predominantly as the reduced immobile phase, elemental Se (Se0), but also as bioavailable organoselenium species, mainly selenomethionine (SeMet). SeMet was also the main species identified within both the Se non-accumulator and Se accumulator plants. The Se soil–plant system in West Limerick is dominated by SeMet, and uptake into the cattle pasture results in selenosis in the grazing dairy herds. The hyperaccumulating Brassica oleracea species could be used to extract both the Se and Mo to reduce the toxicity of the blighted fields.
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Mar 2023
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[18565]
Open Access
Abstract: Myo-inositol tris/tetrakisphosphate kinases (ITPKs) catalyze diverse phosphotransfer reactions with myo-inositol phosphate and myo-inositol pyrophosphate substrates. However, the lack of structures of nucleotide-coordinated plant ITPKs thwarts a rational understanding of phosphotransfer reactions of the family. Arabidopsis possesses a family of four ITPKs of which two isoforms, ITPK1 and ITPK4, control inositol hexakisphosphate and inositol pyrophosphate levels directly or by provision of precursors. Here, we describe the specificity of Arabidopsis ITPK4 to pairs of enantiomers of diverse inositol polyphosphates and show how substrate specificity differs from Arabidopsis ITPK1. Moreover, we provide a description of the crystal structure of ATP-coordinated AtITPK4 at 2.11 Å resolution that along with description of the enantiospecificity of the enzyme affords a molecular explanation for the diverse phosphotransferase activity of this enzyme. That Arabidopsis ITPK4 has a Km for ATP in the tens of micromolar range, potentially explains how, despite the large-scale abolition of InsP6, InsP7 and InsP8 synthesis in Atitpk4 mutants, Atitpk4 lacks the phosphate starvation responses of Atitpk1 mutants. We further demonstrate that Arabidopsis ITPK4 and its homologs in other plants possess an N-terminal haloacid dehalogenase-like fold not previously described. The structural and enzymological information revealed will guide elucidation of ITPK4 function in diverse physiological contexts, including InsP8-dependent aspects of plant biology.
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Mar 2023
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