I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[19800]
Open Access
Abstract: Dye‐decolorizing peroxidases (DyPs) constitute a superfamily of heme‐containing peroxidases that are related neither to animal nor to plant peroxidase families. These are divided into four classes (types A, B, C, and D) based on sequence features. The active site of DyPs contains two highly conserved distal ligands, an aspartate and an arginine, the roles of which are still controversial. These ligands have mainly been studied in class A‐C bacterial DyPs, largely because no effective recombinant expression systems have been developed for the fungal (D‐type) DyPs. In this work, we employ ancestral sequence reconstruction (ASR) to resurrect a D‐type DyP ancestor, AncDyPD‐b1. Expression of AncDyPD‐b1 in Escherichia coli results in large amounts of a heme‐containing soluble protein and allows for the first mutagenesis study on the two distal ligands of a fungal DyP. UV‐Vis and resonance Raman (RR) spectroscopic analyses, in combination with steady‐state kinetics and the crystal structure, reveal fine pH‐dependent details about the heme active site structure and show that both the aspartate (D222) and the arginine (R390) are crucial for hydrogen peroxide reduction. Moreover, the data indicate that these two residues play important but mechanistically different roles on the intraprotein long‐range electron transfer process.
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Jan 2021
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Nathan David
Wright
,
Patrick
Collins
,
Lizbe
Koekemoer
,
Tobias
Krojer
,
Romain
Talon
,
Elliot
Nelson
,
Mingda
Ye
,
Radoslaw
Nowak
,
Joseph
Newman
,
Jia Tsing
Ng
,
Nick
Mitrovic
,
Helton
Wiggers
,
Frank
Von Delft
Open Access
Abstract: Despite the tremendous success of X-ray cryo-crystallography in recent decades, the transfer of crystals from the drops in which they are grown to diffractometer sample mounts remains a manual process in almost all laboratories. Here, the Shifter, a motorized, interactive microscope stage that transforms the entire crystal-mounting workflow from a rate-limiting manual activity to a controllable, high-throughput semi-automated process, is described. By combining the visual acuity and fine motor skills of humans with targeted hardware and software automation, it was possible to transform the speed and robustness of crystal mounting. Control software, triggered by the operator, manoeuvres crystallization plates beneath a clear protective cover, allowing the complete removal of film seals and thereby eliminating the tedium of repetitive seal cutting. The software, either upon request or working from an imported list, controls motors to position crystal drops under a hole in the cover for human mounting at a microscope. The software automatically captures experimental annotations for uploading to the user's data repository, removing the need for manual documentation. The Shifter facilitates mounting rates of 100–240 crystals per hour in a more controlled process than manual mounting, which greatly extends the lifetime of the drops and thus allows a dramatic increase in the number of crystals retrievable from any given drop without loss of X-ray diffraction quality. In 2015, the first in a series of three Shifter devices was deployed as part of the XChem fragment-screening facility at Diamond Light Source, where they have since facilitated the mounting of over 120 000 crystals. The Shifter was engineered to have a simple design, providing a device that could be readily commercialized and widely adopted owing to its low cost. The versatile hardware design allows use beyond fragment screening and protein crystallography.
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Jan 2021
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I05-ARPES
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Wujun
Shi
,
Benjamin J.
Wieder
,
Holger L.
Meyerheim
,
Yan
Sun
,
Yang
Zhang
,
Yiwei
Li
,
Lei
Shen
,
Yanpeng
Qi
,
Lexian
Yang
,
Jagannath
Jena
,
Peter
Werner
,
Klaus
Koepernik
,
Stuart
Parkin
,
Yulin
Chen
,
Claudia
Felser
,
B. Andrei
Bernevig
,
Zhijun
Wang
Abstract: Topological physics and strong electron–electron correlations in quantum materials are typically studied independently. However, there have been rapid recent developments in quantum materials in which topological phase transitions emerge when the single-particle band structure is modified by strong interactions. Here we demonstrate that the room-temperature phase of (TaSe4)2I is a Weyl semimetal with 24 pairs of Weyl nodes. Owing to its quasi-one-dimensional structure, (TaSe4)2I also hosts an established charge-density wave instability just below room temperature. We show that the charge-density wave in (TaSe4)2I couples the bulk Weyl points and opens a bandgap. The correlation-driven topological phase transition in (TaSe4)2I provides a route towards observing condensed-matter realizations of axion electrodynamics in the gapped regime, topological chiral response effects in the semimetallic phase, and represents an avenue for exploring the interplay of correlations and topology in a solid-state material.
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Jan 2021
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I20-EDE-Energy Dispersive EXAFS (EDE)
I20-Scanning-X-ray spectroscopy (XAS/XES)
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Diamond Proposal Number(s):
[17574]
Open Access
Abstract: Deep eutectic solvents (DES) and their hydrated mixtures are used for solvothermal routes towards greener functional nanomaterials. Here we present the first static structural and in situ studies of the formation of iron oxide (hematite) nanoparticles in a DES of choline chloride[thin space (1/6-em)]:[thin space (1/6-em)]urea where xurea = 0.67 (aka. reline) as an exemplar solvothermal reaction, and observe the effects of water on the reaction. The initial speciation of Fe3+ in DES solutions was measured using extended X-ray absorption fine structure (EXAFS), while the atomistic structure of the mixture was resolved from neutron and X-ray diffraction and empirical potential structure refinement (EPSR) modelling. The reaction was monitored using in situ small-angle neutron scattering (SANS), to determine mesoscale changes, and EXAFS, to determine local rearrangements of order around iron ions. It is shown that iron salts form an octahedral [Fe(L)3(Cl)3] complex where (L) represents various O-containing ligands. Solubilised Fe3+ induced subtle structural rearrangements in the DES due to abstraction of chloride into complexes and distortion of H-bonding around complexes. EXAFS suggests the complex forms [–O–Fe–O–] oligomers by reaction with the products of thermal hydrolysis of urea, and is thus pseudo-zero-order in iron. In the hydrated DES, the reaction, nucleation and growth proceeds rapidly, whereas in the pure DES, the reaction initially proceeds quickly, but suddenly slows after 5000 s. In situ SANS and static small-angle X-ray scattering (SAXS) experiments reveal that nanoparticles spontaneously nucleate after 5000 s of reaction time in the pure DES before slow growth. Contrast effects observed in SANS measurements suggest that hydrated DES preferentially form 1D particle morphologies because of choline selectively capping surface crystal facets to direct growth along certain axes, whereas capping is restricted by the solvent structure in the pure DES.
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Jan 2021
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[23480]
Abstract: Although circular helicates can be assembled with a range of labile transition-metal centers, solely “chiral-at-metal” examples (i.e., systems without chiral ligands) and heterometallic (i.e., mixed metal systems, racemic or chiral) circular helicates both remain unexplored. Here, we report on the enantioselective synthesis of a heterometallic (Ir2Zn4) hexameric circular helicate and its elaboration into the corresponding triply interlocked Star of David [2]catenane. The relative inertness of Ir(III) enables enantiospecific synthesis of the hexameric circular helicate using chiral-at-metal building blocks. The resulting Star of David [2]catenane, which is a chiral 6-2-1 link, is formed as a single topological enantiomer. The X-ray crystal structure of the (Ir2Zn4)-catenane shows each of the two 95-atom-long macrocycles entwined around the six metal octahedral metal ions and each other, forming a triply interlocked circular double helix. Two PF6– anions reside above and below the central cavity. The Star of David [2]catenane, both with and without coordinated Zn(II) ions, retains the photophysical properties characteristic of cyclometalated Ir(III) complexes. The synthetic strategy opens up new research directions and opportunities for the assembly of other chiral knots, links, and heterometallic circular helicates.
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Jan 2021
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I15-Extreme Conditions
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Diamond Proposal Number(s):
[22477]
Open Access
Abstract: Defects are emerging as a key tool for fine-tuning the stimuli-responsive behavior of coordination polymers and metal–organic frameworks. Here, we study the ramifications of defects on the mechanical properties of the molecular perovskite [C(NH2)3]MnII(HCOO)3 and its defective analogue [C(NH2)3]Fe2/3III□1/3(HCOO)3, where □ = vacancy. Defects reduce the bulk modulus by 30% and give rise to a temperature-driven phase transition not observed in the nondefective system. The results highlight the opportunities that come with defect-engineering approaches to alter the mechanical properties and underlying thermodynamics, with important implications for the research on stimuli-responsive materials.
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Jan 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Maria-agustina
Rossi
,
Veronica
Martinez
,
Philip
Hinchliffe
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Maria F.
Mojica
,
Valerie
Castillo
,
Diego M.
Moreno
,
Ryan
Smith
,
Brad
Spellberg
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George L.
Drusano
,
Claudia
Banchio
,
Robert A.
Bonomo
,
James
Spencer
,
Alejandro J.
Vila
,
Graciela
Mahler
Diamond Proposal Number(s):
[17212]
Open Access
Abstract: Infections caused by multidrug resistant (MDR) bacteria are a major public health threat. Carbapenems are among the most potent antimicrobial agents that are commercially available to treat MDR bacteria. Bacterial production of carbapenem-hydrolysing metallo-β-lactamases (MBLs) challenges their safety and efficacy, with subclass B1 MBLs hydrolysing almost all β-lactam antibiotics. MBL inhibitors would fulfil an urgent clinical need by prolonging the lifetime of these life-saving drugs. Here we report the synthesis and activity of a series of 2-mercaptomethyl-thiazolidines (MMTZs), designed to replicate MBL interactions with reaction intermediates or hydrolysis products. MMTZs are potent competitive inhibitors of B1 MBLs in vitro (e.g., Ki = 0.44 μM vs. NDM-1). Crystal structures of MMTZ complexes reveal similar binding patterns to the most clinically important B1 MBLs (NDM-1, VIM-2 and IMP-1), contrasting with previously studied thiol-based MBL inhibitors, such as bisthiazolidines (BTZs) or captopril stereoisomers, which exhibit lower, more variable potencies and multiple binding modes. MMTZ binding involves thiol coordination to the Zn(II) site and extensive hydrophobic interactions, burying the inhibitor more deeply within the active site than D/L-captopril. Unexpectedly, MMTZ binding features a thioether–π interaction with a conserved active-site aromatic residue, consistent with their equipotent inhibition and similar binding to multiple MBLs. MMTZs penetrate multiple Enterobacterales, inhibit NDM-1 in situ, and restore carbapenem potency against clinical isolates expressing B1 MBLs. Based on their inhibitory profile and lack of eukaryotic cell toxicity, MMTZs represent a promising scaffold for MBL inhibitor development. These results also suggest sulphur–π interactions can be exploited for general ligand design in medicinal chemistry.
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Jan 2021
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I09-Surface and Interface Structural Analysis
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Diamond Proposal Number(s):
[19067]
Open Access
Abstract: High-end organic–inorganic lead halide perovskite semitransparent p–i–n solar cells for tandem applications use a phenyl-C61-butyric acid methyl ester (PCBM)/atomic layer deposition (ALD)-SnOx electron transport layer stack. Omitting the PCBM would be preferred for manufacturing, but has in previous studies on (FA,MA)Pb(Br,I)3 and (Cs,FA)Pb(Br,I)3 and in this study on Cs0.05FA0.79MA0.16PbBr0.51I2.49 (perovskite) led to poor solar cell performance because of a bias-dependent light-generated current. A direct ALD-SnOx exposure was therefore suggested to form a nonideal perovskite/SnOx interface that acts as a transport barrier for the light-generated current. To further investigate the interface formation during the initial ALD SnOx growth on the perovskite, the mass dynamics of monitor crystals coated by partial p–i–n solar cell stacks were recorded in situ prior to and during the ALD using a quartz crystal microbalance. Two major finds were made. A mass loss was observed prior to ALD for growth temperatures above 60 °C, suggesting the decomposition of the perovskite. In addition, a mostly irreversible mass gain was observed during the first exposure to the Sn precursor tetrakis(dimethylamino)tin(IV) that is independent of growth temperature and that disrupts the mass gain of the following 20–50 ALD cycles. The chemical environments of the buried interface were analyzed by soft and hard X-ray photoelectron spectroscopy for a sample with 50 ALD cycles of SnOx on the perovskite. Although measurements on the perovskite bulk below and the SnOx film above did not show chemical changes, additional chemical states for Pb, Br, and N as well as a decrease in the amount of I were observed in the interfacial region. From the analysis, these states and not the heating of the perovskite were concluded to be the cause of the barrier. This strongly suggests that the detrimental effects can be avoided by controlling the interfacial design.
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Jan 2021
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[16258]
Open Access
Abstract: As a key regulator of the tumour suppressor protein p53, MDM2 is involved in various types of cancer and has thus been an attractive drug target. So far, small molecule design has primarily focussed on the N-terminal p53-binding domain although on-target toxicity effects have been reported. Targeting the catalytic RING domain of MDM2 resembles an alternative approach to drug MDM2 with the idea to prevent MDM2-mediated ubiquitination of p53 while retaining MDM2’s ability to bind p53. The design of RING inhibitors has been limited by the extensive aggregation tendency of the RING domain, making it challenging to undertake co-crystallization attempts with potential inhibitors. Here we compare the purification profiles of the MDM2 RING domain from several species and show that the MDM2 RING domain of other species than human is much less prone to aggregate although the overall structure of the RING domain is conserved. Through sequence comparison and mutagenesis analyses, we identify a single point mutation, G443T, which greatly enhances the dimeric fraction of human MDM2 RING domain during purification. Neither does the mutation alter the structure of the RING domain, nor does it affect E2(UbcH5B)–Ub binding and activity. Hence, MDM2-G443T facilitates studies involving binding partners that would be hampered by the low solubility of the wild-type RING domain. Furthermore, it will be valuable for the development of MDM2 RING inhibitors.
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Jan 2021
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I05-ARPES
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Ryo
Noguchi
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Masaru
Kobayashi
,
Zhanzhi
Jiang
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Kenta
Kuroda
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Takanari
Takahashi
,
Zifan
Xu
,
Daehun
Lee
,
Motoaki
Hirayama
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Masayuki
Ochi
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Tetsuroh
Shirasawa
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Peng
Zhang
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Chun
Lin
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Cédric
Bareille
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Shunsuke
Sakuragi
,
Hiroaki
Tanaka
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So
Kunisada
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Kifu
Kurokawa
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Koichiro
Yaji
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Ayumi
Harasawa
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Viktor
Kandyba
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Alessio
Giampietri
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Alexei
Barinov
,
Timur K.
Kim
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Cephise
Cacho
,
Makoto
Hashimoto
,
Donghui
Lu
,
Shik
Shin
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Ryotaro
Arita
,
Keji
Lai
,
Takao
Sasagawa
,
Takeshi
Kondo
Diamond Proposal Number(s):
[20445]
Abstract: Low-dimensional van der Waals materials have been extensively studied as a platform with which to generate quantum effects. Advancing this research, topological quantum materials with van der Waals structures are currently receiving a great deal of attention. Here, we use the concept of designing topological materials by the van der Waals stacking of quantum spin Hall insulators. Most interestingly, we find that a slight shift of inversion centre in the unit cell caused by a modification of stacking induces a transition from a trivial insulator to a higher-order topological insulator. Based on this, we present angle-resolved photoemission spectroscopy results showing that the real three-dimensional material Bi4Br4 is a higher-order topological insulator. Our demonstration that various topological states can be selected by stacking chains differently, combined with the advantages of van der Waals materials, offers a playground for engineering topologically non-trivial edge states towards future spintronics applications.
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Jan 2021
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