I03-Macromolecular Crystallography
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Daming
Zhou
,
Wanwisa
Dejnirattisai
,
Piyada
Supasa
,
Chang
Liu
,
Alexander J.
Mentzer
,
Helen M.
Ginn
,
Yuguang
Zhao
,
Helen M. E.
Duyvesteyn
,
Aekkachai
Tuekprakhon
,
Rungtiwa
Nutalai
,
Beibei
Wang
,
Guido C.
Paesen
,
Cesar
Lopez-camacho
,
Jose
Slon-campos
,
Bassam
Hallis
,
Naomi
Coombes
,
Kevin
Bewley
,
Sue
Charlton
,
Thomas S.
Walter
,
Donal
Skelly
,
Sheila F.
Lumley
,
Christina
Dold
,
Robert
Levin
,
Tao
Dong
,
Andrew J.
Pollard
,
Julian C.
Knight
,
Derrick
Crook
,
Teresa
Lambe
,
Elizabeth
Clutterbuck
,
Sagida
Bibi
,
Amy
Flaxman
,
Mustapha
Bittaye
,
Sandra
Belij-rammerstorfer
,
Sarah
Gilbert
,
William
James
,
Miles W.
Carroll
,
Paul
Klenerman
,
Eleanor
Barnes
,
Susanna J.
Dunachie
,
Elizabeth E.
Fry
,
Juthathip
Mongkolspaya
,
Jingshan
Ren
,
David I.
Stuart
,
Gavin R.
Screaton
Diamond Proposal Number(s):
[27009]
Open Access
Abstract: The race to produce vaccines against SARS-CoV-2 began when the first sequence was published, and this forms the basis for vaccines currently deployed globally. Independent lineages of SARS-CoV-2 have recently been reported: UK–B.1.1.7, South Africa–B.1.351 and Brazil–P.1. These variants have multiple changes in the immunodominant spike protein which facilitates viral cell entry via the Angiotensin converting enzyme-2 (ACE2) receptor. Mutations in the receptor recognition site on the spike are of great concern for their potential for immune escape. Here we describe a structure-function analysis of B.1.351 using a large cohort of convalescent and vaccinee serum samples. The receptor binding domain mutations provide tighter ACE2 binding and widespread escape from monoclonal antibody neutralization largely driven by E484K although K417N and N501Y act together against some important antibody classes. In a number of cases it would appear that convalescent and some vaccine serum offers limited protection against this variant.
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Feb 2021
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B18-Core EXAFS
B22-Multimode InfraRed imaging And Microspectroscopy
I11-High Resolution Powder Diffraction
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Shaojun
Xu
,
Xue
Han
,
Yujie
Ma
,
Thien D.
Duong
,
Longfei
Lin
,
Emma K.
Gibson
,
Alena
Sheveleva
,
Sarayute
Chansai
,
Alex
Walton
,
Duc-the
Ngo
,
Mark D.
Frogley
,
Chiu C.
Tang
,
Floriana
Tuna
,
Eric J. L.
Mcinnes
,
C. Richard A.
Catlow
,
Christopher
Hardacre
,
Sihai
Yang
,
Martin
Schroeder
Open Access
Abstract: Efficient catalytic conversion of NO2 to non-harmful species remains an important target for research. State-of-the-art deNOx processes are based upon ammonia (NH3)-assisted selective catalytic reduction (NH3-SCR) over Cu-exchanged zeolites at elevated temperatures. Here, we describe a highly efficient non-thermal plasma (NTP) deNOx process catalyzed by a Cu-embedded metal-organic framework, Cu/MFM-300(Al), at room temperature. Under NTP activation at 25°C, Cu/MFM-300(Al) enables direct decomposition of NO2 into N2, NO, N2O, and O2 without the use of NH3 or other reducing agents. NO2 conversion of 96% with a N2 selectivity of 82% at a turnover frequency of 2.9 h−1 is achieved, comparable to leading NH3-SCR catalysts that use NH3 operating at 250°C–550°C. The mechanism for the rate-determining step (NO→N2) is elucidated by in operando diffuse reflectance infrared Fourier transform spectroscopy, and electron paramagnetic resonance spectroscopy confirms the formation of Cu2+⋯NO nitrosylic adducts on Cu/MFM-300(Al), which facilitates NO dissociation and results in the notable N2 selectivity.
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Feb 2021
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[15832]
Open Access
Abstract: The beneficial effects of Cyclooxygenases (COX) inhibitors on human health have been known for thousands of years. Nevertheless, COXs, particularly COX-1, have been linked to a plethora of human diseases such as cancer, heart failure, neurological and neurodegenerative diseases only recently. COXs catalyze the first step in the biosynthesis of prostaglandins (PGs) and are among the most important mediators of inflammation. All published structural work on COX-1 deals with the ovine isoenzyme, which is easier to produce in milligram-quantities than the human enzyme and crystallizes readily. Here, we report the long-sought structure of the human cyclooxygenase-1 (hCOX-1) that we refined to an R/Rfree of 20.82/26.37, at 3.36 Å resolution. hCOX-1 structure provides a detailed picture of the enzyme active site and the residues crucial for inhibitor/substrate binding and catalytic activity. We compared hCOX-1 crystal structure with the ovine COX-1 and human COX-2 structures by using metrics based on Cartesian coordinates, backbone dihedral angles, and solvent accessibility coupled with multivariate methods. Differences and similarities among structures are discussed, with emphasis on the motifs responsible for the diversification of the various enzymes (primary structure, stability, catalytic activity, and specificity). The structure of hCOX-1 represents an essential step towards the development of new and more selective COX-1 inhibitors of enhanced therapeutic potential.
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Feb 2021
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I03-Macromolecular Crystallography
Krios I-Titan Krios I at Diamond
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Wanwisa
Dejnirattisai
,
Daming
Zhou
,
Helen M.
Ginn
,
Helen M. E.
Duyvesteyn
,
Piyada
Supasa
,
James Brett
Case
,
Yuguang
Zhao
,
Thomas
Walter
,
Alexander J.
Mentzer
,
Chang
Liu
,
Beibei
Wang
,
Guido C.
Paesen
,
Jose
Slon-campos
,
César
López-camacho
,
Natasha M.
Kafai
,
Adam L.
Bailey
,
Rita E.
Chen
,
Baoling
Ying
,
Craig
Thompson
,
Jai
Bolton
,
Alex
Fyfe
,
Sunetra
Gupta
,
Tiong Kit
Tan
,
Javier
Gilbert-jaramillo
,
William
James
,
Michael
Knight
,
Miles W.
Carroll
,
Donal
Skelly
,
Christina
Dold
,
Yanchun
Peng
,
Robert
Levin
,
Tao
Dong
,
Andrew J.
Pollard
,
Julian C.
Knight
,
Paul
Klenerman
,
Nigel
Temperton
,
David R.
Hall
,
Mark A.
Williams
,
Neil G.
Paterson
,
Felicity
Bertram
,
C. Alistair
Siebert
,
Daniel K.
Clare
,
Andrew
Howe
,
Julika
Radecke
,
Yun
Song
,
Alain R.
Townsend
,
Kuan-ying A.
Huang
,
Elizabeth E.
Fry
,
Juthathip
Mongkolsapaya
,
Michael S.
Diamond
,
Jingshan
Ren
,
David I.
Stuart
,
Gavin R.
Screaton
Diamond Proposal Number(s):
[27009, 26983]
Open Access
Abstract: Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike, and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC50<0.1μg/ml) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryo-electron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.
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Feb 2021
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[18786, 17375]
Open Access
Abstract: Cadmium cyanide, Cd(CN)2, is a flexible coordination polymer best studied for its strong and isotropic negative thermal expansion (NTE) effect. Here we show that this NTE is actually X-ray-exposure dependent: Cd(CN)2 contracts not only on heating but also on irradiation by X-rays. This behaviour contrasts that observed in other beam-sensitive materials, for which X-ray exposure drives lattice expansion. We call this effect ‘negative X-ray expansion’ (NXE) and suggest its origin involves an interaction between X-rays and cyanide ‘flips’; in particular, we rule out local heating as a possible mechanism. Irradiation also affects the nature of a low-temperature phase transition. Our analysis resolves discrepancies in NTE coefficients reported previously on the basis of X-ray diffraction measurements, and we establish the ‘true’ NTE behaviour of Cd(CN)2 across the temperature range 150–750 K. The interplay between irradiation and mechanical response in Cd(CN)2 highlights the potential for exploiting X-ray exposure in the design of functional materials.
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Feb 2021
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B22-Multimode InfraRed imaging And Microspectroscopy
I11-High Resolution Powder Diffraction
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Lydia
Briggs
,
Ruth
Newby
,
Xue
Han
,
Christopher
Morris
,
Mathew
Savage
,
Cristina
Perez
,
Timothy L.
Easun
,
Mark
Frogley
,
Gianfelice
Cinque
,
Claire A.
Murray
,
Chiu C.
Tang
,
Sihai
Yang
,
Junliang
Sun
,
Martin
Schroeder
Diamond Proposal Number(s):
[22137, 22138]
Open Access
Abstract: We report the adsorption of C2H2, CO2 and SO2 in a new, ultra-stable Cr(III)-based MOF, MFM-300(Cr), {[Cr2(OH)2(L)], H4L = biphenyl-3,3',5,5'-tetracarboxylic acid}. MFM-300(Cr) shows uptakes of 7.37, 7.73 and 8.59 mmol g-1 for CO2, C2H2 and SO2, respectively, at 273 K, 1.0 bar, and shows a higher selectivity for SO2/CO2 compared with the Al(III) analogue MFM-300(Al) (selectivity of 79 vs. 45). In order to monitor the effects of changing metal centre on gas uptake and to integrate the properties of the homometallic analogues, the mixed metal MFM-300(Al0.67Cr0.33), [Al1.34Cr0.66(OH)2L] has been synthesised. In situ synchrotron micro-FTIR spectroscopy has identified distinct CO2 binding environments on Al-O(H)-Al, Cr-O(H)-Cr and Al-O(H)-Cr bridges in MFM-300(Al0.67Cr0.33), and we have determined the binding domains for these gases by in situ synchrotron X-ray diffraction in both MFM-300(Cr) and MFM-300(Al0.67Cr0.33). The capability of these materials for gas separation has been confirmed by dynamic breakthrough experiments. The incorporation of Al(III) and Cr(III) within the same framework allows tuning of the host-guest and guest-guest interactions within these functional porous materials.
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Feb 2021
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I11-High Resolution Powder Diffraction
I12-JEEP: Joint Engineering, Environmental and Processing
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Kieran W. P.
Orr
,
Sean M.
Collins
,
Emily M.
Reynolds
,
Frank
Nightingale
,
Hanna L. B.
Bostroem
,
Simon J.
Cassidy
,
Daniel M.
Dawson
,
Sharon E.
Ashbrook
,
Oxana
Magdysyuk
,
Paul A.
Midgley
,
Andrew L.
Goodwin
,
Hamish H.-m.
Yeung
Diamond Proposal Number(s):
[20946, 18786]
Open Access
Abstract: Control over the spatial distribution of components in metal–organic frameworks has potential to unlock improved performance and new behaviour in separations, sensing and catalysis. We report an unprecedented single-step synthesis of multi-component metal–organic framework (MOF) nanoparticles based on the canonical ZIF-8 (Zn) system and its Cd analogue, which form with a core–shell structure whose internal interface can be systematically tuned. We use scanning transmission electron microscopy, X-ray energy dispersive spectroscopy and a new composition gradient model to fit high-resolution X-ray diffraction data to show how core–shell composition and interface characteristics are intricately controlled by synthesis temperature and reaction composition. Particle formation is investigated by in situ X-ray diffraction, which reveals that the spatial distribution of components evolves with time and is determined by the interplay of phase stability, crystallisation kinetics and diffusion. This work opens up new possibilities for the control and characterisation of functionality, component distribution and interfaces in MOF-based materials.
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Feb 2021
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I16-Materials and Magnetism
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Max
Burian
,
Michael
Porer
,
Jose R. L.
Mardegan
,
Vincent
Esposito
,
Sergii
Parchenko
,
Bulat
Burganov
,
Namrata
Gurung
,
Mahesh
Ramakrishnan
,
Valerio
Scagnoli
,
Hiroki
Ueda
,
Sonia
Francoual
,
Federica
Fabrizi
,
Yoshikazu
Tanaka
,
Tadashi
Togashi
,
Yuya
Kubota
,
Makina
Yabashi
,
Kai
Rossnagel
,
Steven L.
Johnson
,
Urs
Staub
Diamond Proposal Number(s):
[15742]
Open Access
Abstract: In this work, we use ultrafast pump-probe nonresonant and resonant x-ray diffraction to track the periodic lattice distortion and the electronic charge density wave in
1
T
−
TiSe
2
upon optical excitation. We observe a fluence regime in which the periodic lattice deformation is strongly suppressed but the charge density wave related Se
4
p
orbital order remains mostly intact. Complete melting of both structural and electronic order occurs four to five times faster than expected from a purely electronic charge-screening process, strongly suggesting a structurally assisted weakening of excitonic correlations. Our experimental data provide insight on the intricate coupling between structural and electronic order in stabilizing the periodic-lattice-distortion/charge-density-wave state in
1
T
−
TiSe
2
. The results further show that electron-phonon coupling can lead to different, energy dependent phase-transition pathways in condensed matter systems, opening different possibilities in the conception of nonequilibrium phenomena at the ultrafast scale.
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Feb 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[12788]
Open Access
Abstract: The UbiD family of reversible (de)carboxylases depends on the recently discovered prenylated-FMN (prFMN) cofactor for activity. The model enzyme ferulic acid decarboxylase (Fdc1) decarboxylates unsaturated aliphatic acids via a reversible 1,3-cycloaddition process. Protein engineering has extended the Fdc1 substrate range to include (hetero)aromatic acids, although catalytic rates remain poor. This raises the question how efficient decarboxylation of (hetero)aromatic acids is achieved by other UbiD family members. Here, we show that the Pseudomonas aeruginosa virulence attenuation factor PA0254/HudA is a pyrrole-2-carboxylic acid decarboxylase. The crystal structure of the enzyme in the presence of the reversible inhibitor imidazole reveals a covalent prFMN–imidazole adduct is formed. Substrate screening reveals HudA and selected active site variants can accept a modest range of heteroaromatic compounds, including thiophene-2-carboxylic acid. Together with computational studies, our data suggests prFMN covalent catalysis occurs via electrophilic aromatic substitution and links HudA activity with the inhibitory effects of pyrrole-2-carboxylic acid on P. aeruginosa quorum sensing.
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Feb 2021
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NONE-No attached Diamond beamline
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Kenji
Nawa
,
Demie
Kepaptsoglou
,
Arsham
Ghasemi
,
Philip
Hasnip
,
Guillermo
Bárcena-gonzález
,
Giuseppe
Nicotra
,
Pedro L.
Galindo
,
Quentin M.
Ramasse
,
Kohji
Nakamura
,
Susannah C.
Speller
,
Balati
Kuerbanjiang
,
Thorsten
Hesjedal
,
Vlado K.
Lazarov
Abstract: We present a structural and density-functional theory study of the interface of the quasi-twin-free grown three-dimensional topological insulator
Bi
2
Te
3
on Ge(111). Aberration-corrected scanning transmission electron microscopy and electron energy-loss spectroscopy in combination with first-principles calculations show that the weak van der Waals adhesion between the
Bi
2
Te
3
quintuple layer and Ge can be overcome by forming an additional Te layer at their interface. The first-principles calculations of the formation energy of the additional Te layer show it to be energetically favorable as a result of the strong hybridization between the Te and Ge.
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Feb 2021
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