I03-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[28360]
Abstract: Cystathionine γ-lyase (CGL) is a PLP-dependent enzyme that catalyzes the last step of the reverse transsulfuration route for endogenous cysteine biosynthesis. The canonical CGL-catalyzed process consists of an α,γ-elimination reaction that breaks down cystathionine into cysteine, α-ketobutyrate, and ammonia. In some species, the enzyme can alternatively use cysteine as a substrate, resulting in the production of hydrogen sulfide (H2S). Importantly, inhibition of the enzyme and consequently of its H2S production activity, makes multiresistant bacteria considerably more susceptible to antibiotics. Other organisms, such as Toxoplasma gondii, the causative agent of toxoplasmosis, encode a CGL enzyme (TgCGL) that almost exclusively catalyzes the canonical process, with only minor reactivity to cysteine. Interestingly, the substitution of N360 by a serine (the equivalent amino acid residue in the human enzyme) at the active site changes the specificity of TgCGL for the catalysis of cystathionine, resulting in an enzyme that can cleave both the CγS and the CβS bond of cystathionine. Based on these findings and to deepen the molecular basis underlying the enzyme-substrate specificity, we have elucidated the crystal structures of native TgCGL and the variant TgCGL-N360S from crystals grown in the presence of cystathionine, cysteine, and the inhibitor D,L-propargylglycine (PPG). Our structures reveal the binding mode of each molecule within the catalytic cavity and help explain the inhibitory behavior of cysteine and PPG. A specific inhibitory mechanism of TgCGL by PPG is proposed.
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Mar 2023
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Krios I-Titan Krios I at Diamond
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David J. K.
Swainsbury
,
Frederick
Hawkings
,
Elizabeth C.
Martin
,
Sabina
Musial
,
Jack H.
Salisbury
,
Philip J.
Jackson
,
David A.
Farmer
,
Matthew P.
Johnson
,
C. Alistair
Siebert
,
Andrew
Hitchcock
,
C. Neil
Hunter
Diamond Proposal Number(s):
[29785]
Open Access
Abstract: Cytochrome bc1 complexes are ubiquinol:cytochrome c oxidoreductases, and as such, they are centrally important components of respiratory and photosynthetic electron transfer chains in many species of bacteria and in mitochondria. The minimal complex has three catalytic components, which are cytochrome b, cytochrome c1, and the Rieske iron–sulfur subunit, but the function of mitochondrial cytochrome bc1 complexes is modified by up to eight supernumerary subunits. The cytochrome bc1 complex from the purple phototrophic bacterium Rhodobacter sphaeroides has a single supernumerary subunit called subunit IV, which is absent from current structures of the complex. In this work we use the styrene–maleic acid copolymer to purify the R. sphaeroides cytochrome bc1 complex in native lipid nanodiscs, which retains the labile subunit IV, annular lipids, and natively bound quinones. The catalytic activity of the four-subunit cytochrome bc1 complex is threefold higher than that of the complex lacking subunit IV. To understand the role of subunit IV, we determined the structure of the four-subunit complex at 2.9 Å using single particle cryogenic electron microscopy. The structure shows the position of the transmembrane domain of subunit IV, which lies across the transmembrane helices of the Rieske and cytochrome c1 subunits. We observe a quinone at the Qo quinone-binding site and show that occupancy of this site is linked to conformational changes in the Rieske head domain during catalysis. Twelve lipids were structurally resolved, making contacts with the Rieske and cytochrome b subunits, with some spanning both of the two monomers that make up the dimeric complex.
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Mar 2023
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B18-Core EXAFS
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Panpan
Zhang
,
Mingchao
Wang
,
Yannan
Liu
,
Yubin
Fu
,
Mingming
Gao
,
Gang
Wang
,
Faxing
Wang
,
Zhiyong
Wang
,
Guangbo
Chen
,
Sheng
Yang
,
Youwen
Liu
,
Renhao
Dong
,
Minghao
Yu
,
Xing
Lu
,
Xinliang
Feng
Abstract: Although two-dimensional conjugated metal–organic frameworks (2D c-MOFs) provide an ideal platform for precise tailoring of capacitive electrode materials, high-capacitance 2D c-MOFs for non-aqueous supercapacitors remain to be further explored. Herein, we report a novel phthalocyanine-based nickel-bis(dithiolene) (NiS4)-linked 2D c-MOF (denoted as Ni2[CuPcS8]) with outstanding pseudocapacitive properties in 1 M TEABF4/acetonitrile. Each NiS4 linkage is disclosed to reversibly accommodate two electrons, conferring the Ni2[CuPcS8] electrode a two-step Faradic reaction with a record-high specific capacitance among the reported 2D c-MOFs in non-aqueous electrolytes (312 F g–1) and remarkable cycling stability (93.5% after 10,000 cycles). Multiple analyses unveil that the unique electron-storage capability of Ni2[CuPcS8] originates from its localized lowest unoccupied molecular orbital (LUMO) over the nickel-bis(dithiolene) linkage, which allows the efficient delocalization of the injected electrons throughout the conjugated linkage units without inducing apparent bonding stress. The Ni2[CuPcS8] anode is used to demonstrate an asymmetric supercapacitor device that delivers a high operating voltage of 2.3 V, a maximum energy density of 57.4 Wh kg–1, and ultralong stability over 5000 cycles.
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Mar 2023
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I09-Surface and Interface Structural Analysis
I21-Resonant Inelastic X-ray Scattering (RIXS)
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A. S.
Menon
,
B. J.
Johnston
,
S. G.
Booth
,
L.
Zhang
,
K.
Kress
,
B. E.
Murdock
,
G.
Paez Fajardo
,
N. N.
Anthonisamy
,
N.
Tapia-Ruiz
,
S.
Agrestini
,
M.
Garcia-Fernandez
,
K.
Zhou
,
P. K.
Thakur
,
T. L.
Lee
,
A. J.
Nedoma
,
S. A.
Cussen
,
L. F. J.
Piper
Diamond Proposal Number(s):
[29104, 29113]
Open Access
Abstract: The desire to increase the energy density of stoichiometric layered
Li
TM
O
2
(TM = 3d transition metal) cathode materials has promoted investigation into their properties at high states of charge. Although there is increasing evidence for pronounced oxygen participation in the charge compensation mechanism, questions remain whether this is true
O
-redox, as observed in
Li
-excess cathodes. Through a high-resolution
O
K-edge resonant inelastic x-ray spectroscopy (RIXS) study of the
Mn
-free
Ni
-rich layered oxide
Li
Ni
0.98
W
0.02
O
2
, we demonstrate that the same oxidized oxygen environment exists in both
Li
-excess and non-
Li
-excess systems. The observation of identical RIXS loss features in both classes of compounds is remarkable given the differences in their crystallographic structure and delithiation pathways. This lack of a specific structural motif reveals the importance of electron correlation in the charge compensation mechanism for these systems and indicates how a better description of charge compensation in layered oxides is required to understand anionic redox for energy storage.
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Mar 2023
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[29217]
Open Access
Abstract: Metal-organic frameworks (MOFs) are well known for their ability to adsorb various gases. The use of MOFs for the storage and release of biologically active gases, particularly nitric oxide (NO) and carbon monoxide (CO), has been a subject of interest. To elucidate the binding mechanisms and geometry of these gases, an in situ single crystal X-ray diffraction (scXRD) study using synchrotron radiation at Diamond Light Source has been performed on a set of MOFs that display promising gas adsorption properties. NO and CO, were introduced into activated Ni-CPO-27 and the related Co-4,6-dihydroxyisophthalate (Co-4,6-dhip). Both MOFs show strong binding affinity towards CO and NO, however CO suffers more from competitive co-adsorption of water. Additionally, we show that morphology can play an important role in the ease of dehydration for these two systems.
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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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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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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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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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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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