I06-Nanoscience (XPEEM)
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Yang
Li
,
Yan
Wang
,
Andrew F.
May
,
Mauro
Fianchini
,
Chiara
Biz
,
Saeyoung
Oh
,
Yiru
Zhu
,
Hu Young
Jeong
,
Jieun
Yang
,
Jose
Gracia
,
Manish
Chhowalla
Diamond Proposal Number(s):
[33245]
Open Access
Abstract: Spin selective catalysis is an emerging approach for improving the thermodynamics and kinetics of reactions. The role of electron spins has been scarcely studied in catalytic reactions. One exception is the oxygen evolution reaction (OER) where strongly correlated metals and oxides are used as catalysts. In OER, spin alignment facilitates the transition of singlet state of the reactant to the triplet state of O2. However, the influence of strong correlations on spin exchange mechanism and spin selective thermodynamics of most catalytic reactions remain unclear. Here we decouple the strongly correlated catalyst from the electrolyte to study spin exchange in two-dimensional (2D) magnetic iron germanium telluride (FGT) heterostructure. We demonstrate that transmission of spin and electrochemical information between the catalyst and the reactant can occur through quantum exchange interaction despite the catalyst of FGT being completely encapsulated by graphene or hexagonal boron nitride (hBN). The strong correlations in FGT that lead to enhanced spin exchange in OER are observed in graphene or hBN layers with thicknesses of up to 6 nm. We demonstrate that spin alignment in FGT leads to a lowering of thermodynamic barrier for adsorption of hydroxide ion and electron transfer to the catalyst. This results in up to fivefold enhancement in OER performance and improved kinetics. Our results provide clear evidence that transmission of both quantum mechanical and electrochemical information through quantum spin exchange interaction in FGT leads to an enhancement in catalytic performance.
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Dec 2024
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B18-Core EXAFS
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Nivetha
Jeyachandran
,
Wangchao
Yuan
,
Xiang
Li
,
Akshayini
Muthuperiyanayagam
,
Stefania
Gardoni
,
Jiye
Feng
,
Qingsheng
Gao
,
Martin
Wilding
,
Peter
Wells
,
Devis
Di Tommaso
,
Cristina
Giordano
Diamond Proposal Number(s):
[29721]
Open Access
Abstract: The rising levels of CO2 have spurred growing concerns for our environment, and curbing CO2 emissions may not be practically viable with the expanding human population. One attractive strategy is the electrochemical CO2 reduction (CO2RR) into value added chemicals but because of the chemical inertness of the CO2 molecule, the electrochemical reduction requires a suitable catalyst. Cu-based catalysts have been largely investigated for CO2RR, however, the difficulty achieving a high selectivity and faradaic efficiency towards specific products, especially hydrocarbons, is still a challenge, alongside the concern over cost, stability and scarcity of the metal catalyst. The present research focuses on tuning the crystallinity of Cu nanoparticles via a green, cost-friendly, and facile method, called the urea glass route. Remarkably, the incorporation of a selected nitrogen-carbon rich source (namely, 4,5 dicyanoimidazole) at low temperatures allow the formation of an oxidized derived amorphous Cu system, whilst a second thermal treatment enables the transformation to crystalline Cu0. We found that the combination of surface Cu0 and Cu1+ (observed via XPS studies) present in our amorphous and crystalline Cu nanoparticles leads to interesting differences in the final catalytic activity when tested under CO2 reaction conditions. The combination of extended X-ray absorption fine structure (EXAFS) experiments and molecular dynamics simulations provides compelling evidence for the amorphous and metallic nature of Cu nanoparticles.
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Dec 2024
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Eugene
Kuatsjah
,
Alexa
Schwartz
,
Michael
Zahn
,
Konstantinos
Tornesakis
,
Zoe A.
Kellermyer
,
Morgan A.
Ingraham
,
Sean P.
Woodworth
,
Kelsey J.
Ramirez
,
Paul A.
Cox
,
Andrew R.
Pickford
,
Davinia
Salvachúa
Diamond Proposal Number(s):
[23269]
Open Access
Abstract: White-rot fungi (WRF) are the most efficient lignin-degrading organisms in nature. However, their capacity to use lignin-related aromatic compounds, such as 4-hydroxybenzoate, as carbon sources has only been described recently. Previously, the hydroxyquinol pathway was proposed for the bioconversion of these compounds in fungi, but gene- and structure-function relationships of the full enzymatic pathway remain uncharacterized in any single fungal species. Here, we characterize seven enzymes from two WRF, Trametes versicolor and Gelatoporia subvermispora, which constitute a four-enzyme cascade from 4-hydroxybenzoate to β-ketoadipate via the hydroxyquinol pathway. Furthermore, we solve the crystal structure of four of these enzymes and identify mechanistic differences with the closest bacterial and fungal structural homologs. Overall, this research expands our understanding of aromatic catabolism by WRF and establishes an alternative strategy for the conversion of lignin-related compounds to the valuable molecule β-ketoadipate, contributing to the development of biological processes for lignin valorization.
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Dec 2024
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I24-Microfocus Macromolecular Crystallography
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Maria Elena
Laugieri
,
Immacolata
Speciale
,
Ana
Gimeno
,
Sicheng
Lin
,
Brock W.
Byers
,
Ana
Poveda
,
Reyes
Núñez‐franco
,
Idoia
Iturrioz
,
María J.
Moure
,
Gonzalo
Jiménez-Osés
,
Irene
Russo‐krauss
,
Anna
Notaro
,
James L.
Van Etten
,
Todd L.
Lowary
,
Jesús
Jimenez-Barbero
,
Cristina
De Castro
,
Michela
Tonetti
,
Adriana L.
Rojas
Diamond Proposal Number(s):
[20113]
Open Access
Abstract: Protein A075L is a β-xylosyltransferase that participates in producing the core of the N-glycans found in VP54, the major viral capsid protein of Paramecium bursaria chlorella virus-1 (PBCV-1). In this study, we present an X-ray crystallographic analysis of the apo form of A075L, along with its complexes with the sugar donor and with a trisaccharide acceptor. The protein structure shows a typical GT-B folding, with two Rossmann-like fold domains, in which the acceptor substrate binds to the N-terminal region, and the nucleotide-sugar donor binds to the C-terminal region. We propose that the catalytic mechanism follows a direct displacement SN2-like reaction, where Asp73 serves as a catalytic base that deprotonates the incoming nucleophile of the acceptor, facilitating direct displacement of the UDP with the inversion of the anomeric configuration of the acceptor without metal ion dependence, while the interactions with side chains of Arg158 and Arg208 stabilize the developing negative charge. Using isothermal titration calorimetry, nuclear magnetic resonance spectroscopy, high-performance liquid chromatography, and molecular dynamics simulations, the catalytic activity and specificity of this enzyme have been unraveled.
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Dec 2024
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[34808]
Open Access
Abstract: Tripartite ATP-independent periplasmic (TRAP) transporters are widespread in prokaryotes and are responsible for the transport of a variety of different ligands, primarily organic acids. TRAP transporters can be divided into two subclasses; DctP-type and TAXI type, which share the same overall architecture and substrate-binding protein requirement. DctP-type transporters are very well studied and have been shown to transport a range of compounds including dicarboxylates, keto acids, and sugar acids. However, TAXI-type transporters are relatively poorly understood. To address this gap in our understanding, we have structurally and biochemically characterized VC0430 from Vibrio cholerae. We show it is a monomeric, high affinity glutamate-binding protein, which we thus rename VcGluP. VcGluP is stereoselective, binding the L-isomer preferentially, and can also bind L-glutamine and L-pyroglutamate with lower affinity. Structural characterization of ligand-bound VcGluP revealed details of its binding site and biophysical characterization of binding site mutants revealed the substrate binding determinants, which differ substantially from those of DctP-type TRAPs. Finally, we have analyzed the interaction between VcGluP and its cognate membrane component, VcGluQM (formerly VC0429) in silico, revealing an architecture hitherto unseen. To our knowledge, this is the first transporter in V. cholerae to be identified as specific to glutamate, which plays a key role in the osmoadaptation of V. cholerae, making this transporter a potential therapeutic target.
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Dec 2024
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I19-Small Molecule Single Crystal Diffraction
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Mariya
Aleksich
,
Yeongsu
Cho
,
Daniel W.
Paley
,
Maggie C.
Willson
,
Hawi N.
Nyiera
,
Patience A.
Kotei
,
Vanessa
Oklejas
,
David W.
Mittan-Moreau
,
Elyse A.
Schriber
,
Kara
Christensen
,
Ichiro
Inoue
,
Shigeki
Owada
,
Kensuke
Tono
,
Michihiro
Sugahara
,
Satomi
Inaba-Inoue
,
Mohammad
Vakili
,
Christopher J.
Milne
,
Fabio
Dallantonia
,
Dmitry
Khakhulin
,
Fernando
Ardana-Lamas
,
Frederico
Lima
,
Joana
Valerio
,
Huijong
Han
,
Tamires
Gallo
,
Hazem
Yousef
,
Oleksii
Turkot
,
Ivette J. Bermudez
Macias
,
Thomas
Kluyver
,
Philipp
Schmidt
,
Luca
Gelisio
,
Adam R.
Round
,
Yifeng
Jiang
,
Doriana
Vinci
,
Yohei
Uemura
,
Marco
Kloos
,
Adrian P.
Mancuso
,
Mark
Warren
,
Nicholas K.
Sauter
,
Jing
Zhao
,
Tess
Smidt
,
Heather J.
Kulik
,
Sahar
Sharifzadeh
,
Aaron S.
Brewster
,
J. Nathan
Hohman
Diamond Proposal Number(s):
[35300]
Abstract: X-ray free electron laser (XFEL) microcrystallography and synchrotron single-crystal crystallography are used to evaluate the role of organic substituent position on the optoelectronic properties of metal–organic chalcogenolates (MOChas). MOChas are crystalline 1D and 2D semiconducting hybrid materials that have varying optoelectronic properties depending on composition, topology, and structure. While MOChas have attracted much interest, small crystal sizes impede routine crystal structure determination. A series of constitutional isomers where the aryl thiol is functionalized by either methoxy or methyl ester are solved by small molecule serial femtosecond X-ray crystallography (smSFX) and single crystal rotational crystallography. While all the methoxy examples have a low quantum yield (0-1%), the methyl ester in the ortho position yields a high quantum yield of 22%. The proximity of the oxygen atoms to the silver inorganic core correlates to a considerable enhancement of quantum yield. Four crystal structures are solved at a resolution range of 0.8–1.0 Å revealing a collapse of the 2D topology for functional groups in the 2- and 3- positions, resulting in needle-like crystals. Further analysis using density functional theory (DFT) and many-body perturbation theory (MBPT) enables the exploration of complex excitonic phenomena within easily prepared material systems.
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Dec 2024
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B21-High Throughput SAXS
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Sarah-Ana
Mitrovic
,
Chamalee
Demalgiriya-Gamage
,
Lisa-Maria
Winter
,
Tobias
Kiechle
,
Rebecca
Ebenhoch
,
Heike
Neubauer
,
Birgit
Stierstorfer
,
Lee
Frego
,
Christian
Wolfrum
,
Sophia
Reindl
,
Herbert
Nar
Open Access
Abstract: GOLD domain seven-transmembrane helix (GOST) proteins form a new protein family involved in trafficking of membrane-associated cargo. They share a characteristic extracellular/luminal Golgi-dynamics (GOLD) domain, possibly responsible for ligand recognition. Based on structural homology, GPR180 is a new member of this protein family, but little is known about the cellular role of GPR180. Here we show the X-ray structure of the N-terminal domain of GPR180 (1.9 Å) and can confirm the homology to GOLD domains. Using cellular imaging we show the localization of GPR180 in intracellular vesicular structures implying its exposure to acidic pH environments. With Hydrogen/Deuterium Exchange-Mass Spectrometry (HDX-MS) we identify pH-dependent conformational changes, which can be mapped to a putative ligand binding site in the transmembrane region. The results reveal GPR180’s role in intracellular vesicles and offer insights into the pH-dependent function of this conserved GOST protein.
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Dec 2024
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I20-EDE-Energy Dispersive EXAFS (EDE)
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Abstract: The development and growth of heterogeneous catalysis are directly connected to the knowledge of the structure and associated changes that arise from reactions it has, under specific environmental conditions. In liquid phase catalysed reactions, which was the focus of this thesis, information associated with the reaction, e.g. the active site, is often difficult to obtain due to the solvent being present at higher quantities in comparison to the much smaller quantity of active species. Additionally, difficulties associated with the characterisation of such systems arise from the frequently short lifetime of active species, and the tendency of catalytic events to occur on the surface of the catalyst, with the bulk structure barely participating in any reactions. The purpose of this thesis was to conduct a research study, integrating modulation excitation (ME) approach with total neutron scattering (TNS) and X-ray absorption spectroscopy (XAS) techniques. The combination of periodic modulation excitation with phase-sensitive detection (PSD) analysis, and their integration within TNS and XAS, allowed us to probe surface structural changes. This approach demonstrated an enhanced signal-to-noise ratio of the experimental data and significantly improved the sensitivity of the respective instruments to weak component contributions. Periodic electrical potential switches were employed as external stimulations to perturb the investigated systems reversibly and measure the active species contributions. In contrast to XAS, where ME methodology has been extensively implemented to the study of gas-phase catalytic reactions and most recently to liquid-phase catalytic reactions; combined ME-TNS studies is a novel approach that was successfully developed and demonstrated for the first time in this thesis. Ultimately, the essential instrumentation and innovative analysis procedures to extract useful structural information from the newly acquired ME-TNS data are demonstrated in the results chapters of this thesis. Finally, the ME technique was implemented at the Energy Dispersive EXAFS (EDE) branch of the I20 X-ray absorption spectroscopy beamline at Diamond Light Source, while the NIMROD instrument at ISIS neutron and muon source was developed to enable it to obtain ME-neutron scattering data.
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Dec 2024
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I24-Microfocus Macromolecular Crystallography
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Open Access
Abstract: Protein–inhibitor crystal structures aid medicinal chemists in efficiently improving the potency and selectivity of small-molecule inhibitors. It is estimated that a quarter of lead molecules in drug discovery projects are halogenated. Protein–inhibitor crystal structures have shed light on the role of halogen atoms in ligand binding. They form halogen bonds with protein atoms and improve shape complementarity of inhibitors with protein binding sites. However, specific radiation damage (SRD) can cause cleavage of carbon–halogen (C–X) bonds during X-ray diffraction data collection. This study shows significant C–X bond cleavage in protein–ligand structures of the therapeutic cancer targets B-cell lymphoma 6 (BCL6) and heat shock protein 72 (HSP72) complexed with halogenated ligands, which is dependent on the type of halogen and chemical structure of the ligand. The study found that metrics used to evaluate the fit of the ligand to the electron density deteriorated with increasing X-ray dose, and that SRD eliminated the anomalous signal from brominated ligands. A point of diminishing returns is identified, where collecting highly redundant data reduces the anomalous signal that may be used to identify binding sites of low-affinity ligands or for experimental phasing. Straightforward steps are proposed to mitigate the effects of C–X bond cleavage on structures of proteins bound to halogenated ligands and to improve the success of anomalous scattering experiments.
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Dec 2024
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I13-2-Diamond Manchester Imaging
I14-Hard X-ray Nanoprobe
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Kamila
Iskhakova
,
Hanna
Cwieka
,
Svenja
Meers
,
Heike
Helmholz
,
Anton
Davydok
,
Malte
Storm
,
Ivo Matteo
Baltruschat
,
Silvia
Galli
,
Daniel
Pröfrock
,
Olga
Will
,
Mirko
Gerle
,
Timo
Damm
,
Sandra
Sefa
,
Weilue
He
,
Keith
Macrenaris
,
Malte
Soujon
,
Felix
Beckmann
,
Julian
Moosmann
,
Thomas
O'Hallaran
,
Roger J.
Guillory
,
D. C. Florian
Wieland
,
Berit
Zeller-Plumhoff
,
Regine
Willumeit-Römer
Diamond Proposal Number(s):
[25078]
Open Access
Abstract: Magnesium (Mg) – based alloys are becoming attractive materials for medical applications as temporary bone implants for support of fracture healing, e.g. as a suture anchor. Due to their mechanical properties and biocompatibility, they may replace titanium or stainless-steel implants, commonly used in orthopedic field. Nevertheless, patient safety has to be assured by finding a long-term balance between metal degradation, osseointegration, bone ultrastructure adaptation and element distribution in organs. In order to determine the implant behavior and its influence on bone and tissues, we investigated two Mg alloys with gadolinium contents of 5 and 10 wt percent in comparison to permanent materials titanium and polyether ether ketone. The implants were present in rat tibia for 10, 20 and 32 weeks before sacrifice of the animal. Synchrotron radiation-based micro computed tomography enables the distinction of features like residual metal, degradation layer and bone structure. Additionally, X-ray diffraction and X-ray fluorescence yield information on parameters describing the bone ultrastructure and elemental composition at the bone-to-implant interface. Finally, with element specific mass spectrometry, the elements and their accumulation in the main organs and tissues are traced. The results show that Mg-xGd implants degrade in vivo under the formation of a stable degradation layer with bone remodeling similar to that of Ti after 10 weeks. No accumulation of Mg and Gd was observed in selected organs, except for the interfacial bone after 8 months of healing. Thus, we confirm that Mg-5Gd and Mg-10Gd are suitable material choices for bone implants.
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Nov 2024
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