I14-Hard X-ray Nanoprobe
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Kazuya
Morooka
,
Eitaro
Kurihara
,
Masato
Takehara
,
Ryu
Takami
,
Kazuki
Fueda
,
Kenji
Horie
,
Mami
Takehara
,
Shinya
Yamasaki
,
Toshihiko
Ohnuki
,
Bernd
Grambow
,
Gareth T. W.
Law
,
Joyce W. I.
Ang
,
William R.
Bower
,
Julia
Parker
,
Rodney
Ewings
,
Satoshi
Utsunomiya
Diamond Proposal Number(s):
[21246]
Abstract: A contaminated zone elongated toward Futaba Town, north-northwest of the Fukushima Daiichi Nuclear Power Plant (FDNPP), contains highly radioactive particles released from reactor Unit 1. There are uncertainties associated with the physio-chemical properties and environmental impacts of these particles. In this study, 31 radioactive particles were isolated from surface soils collected 3.9 km north-northwest of the FDNPP. Two of these particles have the highest particle-associated 134+137Cs activity ever reported for Fukushima (6.1 × 105 and 2.5 × 106 Bq per particle after decay-correction to March, 2011). The new, highly-radioactive particle labeled FTB1 is an aggregate of flaky silicate nanoparticles with an amorphous structure containing ~0.8 wt% Cs, occasionally associated with SiO2 and TiO2 inclusions. FTB1 likely originates from the reactor building, which was damaged by a H2 explosion, after adsorbing volatilized Cs. The 134+137Cs activity in the other highly radioactive particle labeled FTB26 exceeded 106 Bq. FTB26 has a glassy carbon core and a surface that is embedded with numerous micro-particles: Pb–Sn alloy, fibrous Al-silicate, Ca-carbonate or hydroxide, and quartz. The isotopic signatures of the micro-particles indicate neutron capture by B, Cs volatilization, and adsorption of natural Ba. The composition of the micro-particles on FTB26 reflects the composition of airborne particles at the moment of the H2 explosion. Owing to their large size, the health effects of the highly radioactive particles are likely limited to external radiation during static contact with skin; the highly radioactive particles are thus expected to have negligible health impacts for humans. By investigating the mobility of the highly radioactive particles, we can better understand how the radiation dose transfers through environments impacted by Unit 1. The highly radioactive particles also provide insights into the atmospheric conditions at the time of the Unit 1 explosion and the physio-chemical phenomena that occurred during reactor meltdown.
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Feb 2021
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[25402]
Open Access
Abstract: For several centuries, microorganisms and enzymes have been used for many different applications. Although many enzymes with industrial applications have already been reported, different screening technologies, methods and approaches are constantly being developed in order to allow the identification of enzymes with even more interesting applications. In our work, we have performed data mining on the Chitinophaga sp. genome, a gram-negative bacterium isolated from a bacterial consortium of sugarcane bagasse isolated from an ethanol plant. The analysis of 8 Mb allowed the identification of the chtcp gene, previously annotated as putative Cht4039. The corresponding codified enzyme, denominated as ChtCP, showed the HEXXH conserved motif of family M32 from thermostable carboxypeptidases. After expression in E. coli, the recombinant enzyme was characterized biochemically. ChtCP showed the highest activity versus benziloxicarbonil Ala-Trp at pH 7.5, suggesting a preference for hydrophobic substrates. Surprisingly, the highest activity of ChtCP observed was between 55 °C and 75 °C, and 62% activity was still displayed at 100 °C. We observed that Ca2+, Ba2+, Mn2+ and Mg2+ ions had a positive effect on the activity of ChtCP, and an increase of 30 °C in the melting temperature was observed in the presence of Co2+. These features together with the structure of ChtCP at 1.2 Å highlight the relevance of ChtCP for further biotechnological applications.
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Feb 2021
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I02-Macromolecular Crystallography
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Abstract: Anisotropic environments can drastically alter the spectroscopy and photochemistry of molecules, leading to complex structure‐function relationships. We examined this using fluorescent proteins as easy‐to‐modify model systems. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, including the determination of 43 crystal structures. Correlation and principal component analysis confirmed the complex relationship between structure and spectroscopy, but also allowed us to identify consistent trends and to relate these to the spatial organization. We find that changes in spectroscopic properties can come about through multiple underlying mechanisms, of which polarity, hydrogen bonding and presence of water molecules are key modulators. We anticipate that our findings and rich structure/spectroscopy dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.
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Feb 2021
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[23620]
Open Access
Abstract: UTP-glucose-1-phosphate uridylyltransferases (UGPases) are enzymes that produce UDP-glucose from UTP and glucose-1-phosphate. In Bacillus subtilis 168, UDP-glucose is required for the decoration of wall teichoic acid (WTA) with glucose residues and the formation of glucolipids. The B. subtilis UGPase GtaB is essential for UDP-glucose production under standard aerobic growth conditions, and gtaB mutants display severe growth and morphological defects. However, bioinformatics predictions indicate that two other UGPases, are present in B. subtilis. Here, we investigated the function of one of them named YngB. The crystal structure of YngB revealed that the protein has the typical fold and all necessary active site features of a functional UGPase. Furthermore, UGPase activity could be demonstrated in vitro using UTP and glucose-1-phosphate as substrates. Expression of YngB from a synthetic promoter in a B. subtilis gtaB mutant resulted in the reintroduction of glucose residues on WTA and production of glycolipids, demonstrating that the enzyme can function as UGPase in vivo. When wild-type and mutant B. subtilis strains were grown under anaerobic conditions, YngB-dependent glycolipid production and glucose decorations on WTA could be detected, revealing that YngB is expressed from its native promoter under anaerobic condition. Based on these findings, along with the structure of the operon containing yngB and the transcription factor thought to be required for its expression, we propose that besides WTA, potentially other cell wall components might be decorated with glucose residues during oxygen limited growth condition.
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Feb 2021
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[27906]
Open Access
Abstract: Multicomponent hydrogels offer a tremendous opportunity to prepare useful and exciting materials that cannot be accessed using a single component. Here, we describe an unusual multi‐component low molecular weight gelling system that exhibits pH‐responsive behavior involving cooperative hydrogen bonding between the components, allowing it to maintain a gel phase across a wide pH range. Unlike traditional acid‐triggered gels, our system undergoes a change in the underlying molecular packing and maintains the β‐sheet structure both at acidic and basic pH. We further establish that autonomous programming between these two gel states is possible by an enzymatic reaction which allows us to prepare gels with improved mechanical properties.
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Feb 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Emerald S.
Ellis
,
Daniel J.
Hinchen
,
Alissa
Bleem
,
Lintao
Bu
,
Sam J. B.
Mallinson
,
Mark D.
Allen
,
Bennett R.
Streit
,
Melodie M.
Machovina
,
Quinlan V.
Doolin
,
William E.
Michener
,
Christopher W.
Johnson
,
Brandon C.
Knott
,
Gregg T.
Beckham
,
John E.
Mcgeehan
,
Jennifer L.
Dubois
Diamond Proposal Number(s):
[17212, 23269]
Open Access
Abstract: Biological funneling of lignin-derived aromatic compounds is a promising approach for valorizing its catalytic depolymerization products. Industrial processes for aromatic bioconversion will require efficient enzymes for key reactions, including demethylation of O-methoxy-aryl groups, an essential and often rate-limiting step. The recently characterized GcoAB cytochrome P450 system comprises a coupled monoxygenase (GcoA) and reductase (GcoB) that catalyzes oxidative demethylation of the O-methoxy-aryl group in guaiacol. Here, we evaluate a series of engineered GcoA variants for their ability to demethylate o-and p-vanillin, which are abundant lignin depolymerization products. Two rationally designed, single amino acid substitutions, F169S and T296S, are required to convert GcoA into an efficient catalyst toward the o- and p-isomers of vanillin, respectively. Gain-of-function in each case is explained in light of an extensive series of enzyme-ligand structures, kinetic data, and molecular dynamics simulations. Using strains of Pseudomonas putida KT2440 already optimized for p-vanillin production from ferulate, we demonstrate demethylation by the T296S variant in vivo. This work expands the known aromatic O-demethylation capacity of cytochrome P450 enzymes toward important lignin-derived aromatic monomers.
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Feb 2021
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I19-Small Molecule Single Crystal Diffraction
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Estefanía
Tiburcio
,
Rossella
Greco
,
Marta
Mon
,
Jordi
Ballesteros-soberanas
,
Jesus
Ferrando-soria
,
Juan-carlos
Hernandez-garrido
,
Judit
Oliver-meseguer
,
Carlo
Marini
,
Mercedes
Boronat
,
Donatella
Armentano
,
Antonio
Leyva-perez
,
Emilio
Pardo
,
Miguel
López-haro
Diamond Proposal Number(s):
[18768, 22411]
Abstract: Metal single-atom catalysts (SACs) promise great rewards in terms of
metal atom efficiency. However, the requirement of particular conditions and
supports for their synthesis, together with the need of solvents and additives for
catalytic implementation, often precludes their use under industrially viable
conditions. Here, we show that palladium single atoms are spontaneously formed
after dissolving tiny amounts of palladium salts in neat benzyl alcohols, to catalyze
their direct aerobic oxidation to benzoic acids without ligands, additives, or solvents.
With this result in hand, the gram-scale preparation and stabilization of Pd SACs
within the functional channels of a novel methyl-cysteine-based metal−organic
framework (MOF) was accomplished, to give a robust and crystalline solid catalyst
fully characterized with the help of single-crystal X-ray diffraction (SCXRD). These
results illustrate the advantages of metal speciation in ligand-free homogeneous organic reactions and the translation into solid
catalysts for potential industrial implementation.
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Feb 2021
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[27011]
Abstract: A two-phase near-β titanium alloy (Ti–10V–2Fe–3Al, or Ti-1023) in its as-forged state is employed to illustrate the feasibility of a Bayesian framework to identify single-crystal elastic constants (SEC). High Energy X-ray diffraction (HE-XRD) obtained at the Diamond synchrotron source are used to characterize the evolution of lattice strains for various grain orientations during in situ specimen loading in the elastic regime. On the other hand, specimen behavior and grain deformation are estimated using the elastic self-consistent (ELSC) homogenization scheme. The XRD data and micromechanical modelling are revisited with a Bayesian framework. The effect of different material parameters (crystallographic and morphological textures, phase volume fraction) of the micromechanical model and the biases introduced by the XRD data on the identification of the SEC of the β phase are systematically investigated. In this respect, all the three cubic elastic constants of the β phase (
) in the Ti-1023 alloy have been derived with their uncertainties. The grain aspect ratio in the ELSC model, which is often not considered in the literature, is found to be an important parameter in affecting the identified SEC. The Bayesian inference suggests a high probability for non-spherical grains (aspect ratio of
):
. The uncertainty obtained by Bayesian approach lies in the range of ∼1-3 GPa for the shear modulus
, and ∼7 GPa for the shear modulus
, while it is significantly larger in the case of the bulk modulus
(∼17-24 GPa).
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Feb 2021
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[13467]
Open Access
Abstract: Microbial plant pathogens secrete effector proteins which manipulate the host to promote infection. Effectors can be recognised by plant intracellular nucleotide-binding leucine-rich repeat (NLR) receptors, initiating an immune response. The AVR-Pik effector from the rice blast fungus Magnaporthe oryzae is recognised by a pair of rice NLR receptors, Pik-1 and Pik-2. Pik-1 contains a non-canonical integrated heavy metal-associated (HMA) domain, which directly binds AVR-Pik to activate plant defences. The host targets of AVR-Pik are also HMA domain-containing proteins, namely heavy metal-associated isoprenylated plant proteins (HIPPs) and heavy metal-associated plant proteins (HPPs). Here, we demonstrate that one of these targets interacts with a wider set of AVR-Pik variants compared to the Pik-1 HMA domains. We define the biochemical and structural basis of the interaction between AVR-Pik and OsHIPP19, and compare the interaction to that formed with the HMA domain of Pik-1. Using analytical gel filtration and surface plasmon resonance, we show that multiple AVR-Pik variants, including the stealthy variants AVR-PikC and AVR-PikF which do not interact with any characterised Pik-1 alleles, bind to OsHIPP19 with nanomolar affinity. The crystal structure of OsHIPP19 in complex with AVR-PikF reveals differences at the interface that underpin high-affinity binding of OsHIPP19-HMA to a wider set of AVR-Pik variants than achieved by the integrated HMA domain of Pik-1. Our results provide a foundation for engineering the HMA domain of Pik-1 to extend binding to currently unrecognised AVR-Pik variants and expand disease resistance in rice to divergent pathogen strains.
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Feb 2021
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B22-Multimode InfraRed imaging And Microspectroscopy
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Diamond Proposal Number(s):
[17044]
Abstract: Bis(2-ethylhexyl) phosphate (BEHP) was exposed to carbon steel surfaces from dry and water-saturated dodecane. The resulting changes to the surfaces were characterised using spectroscopic techniques (energy dispersive X-ray (EDX), X-ray photoelectron (XPS), and far-infrared reflection absorption (RAIRS) spectroscopies) and polarised neutron reflectometry (PNR). Although there was no observable affinity of BEHP to the steel surface in dry solvent, a layer of rough iron (III) phosphate formed in water-saturated dodecane. The phosphate-reacted steel surface showed some resistance to corrosion by seawater, suggesting the formation of a cohesive barrier against corrosive species. The results support the use of BEHP as an anti-corrosion additive and a viable phosphating agent for steel surfaces.
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Feb 2021
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