I07-Surface & interface diffraction
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Diamond Proposal Number(s):
[22176]
Abstract: Hypothesis: Despite the widespread industrial usage of erucamide as a slip additive to modify polymer surface properties, a controversy appears to have persisted regarding the nanostructure of erucamide surface layers, particularly the molecular orientation at the outermost layer. The erucamide nanostructure and molecular orientation, along with its surface coverage, hydrophobicity, and adhesive response, can be tuned by simply varying the erucamide concentration in the solution from which the spin coated layer is prepared. Experiments: Synchrotron X-ray reflectivity (XRR) allowed a comprehensive characterisation of the out-of-plane structural parameters (e.g. molecular packing and thickness) of the erucamide layers prepared via spin coating from nonaqueous solution on silica. Complementary Atomic Force Microscopy (AFM) imaging with high lateral resolution revealed localised in-plane structures. Contact angle measurements provided information on the wettability of erucamide-coated surfaces. Peak Force Quantitative Nanomechanical Mapping (QNM) allowed a correlation between the erucamide nanostructure with the surface nanomechanical properties (i.e. adhesive response). Findings: Our results reveal erucamide surface nanostructures on silica as patchy monolayers, isolated circular bilayers/rounded rectangle-like aggregates and overlapping plate-like multilayers as the erucamide concentration in the spin coating solution was varied. In all the cases, XRR and AFM results were consistent with the picture that the erucamide tails were oriented outwards. The QNM adhesion force mapping of all the observed morphologies also supported this molecular orientation at the outermost erucamide monolayer. The wettability study further confirmed this conclusion with the observed increase in the surface hydrophobicity and coverage upon increasing erucamide concentration, with the macroscopic water contact angle θ = 92.9° ± 2.9° at the highest erucamide concentration of 2 wt%.
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May 2021
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Krios II-Titan Krios II at Diamond
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Yasunori
Watanabe
,
Luiza
Mendonca
,
Elizabeth R.
Allen
,
Andrew
Howe
,
Mercede
Lee
,
Joel D.
Allen
,
Himanshi
Chawla
,
David
Pulido
,
Francesca
Donnellan
,
Hannah
Davies
,
Marta
Ulaszewska
,
Sandra
Belij-Rammerstorfer
,
Susan
Morris
,
Anna-Sophia
Krebs
,
Wanwisa
Dejnirattisai
,
Juthathip
Mongkolsapaya
,
Piyada
Supasa
,
Gavin R.
Screaton
,
Catherine M.
Green
,
Teresa
Lambe
,
Peijun
Zhang
,
Sarah C.
Gilbert
,
Max
Crispin
Diamond Proposal Number(s):
[18477, 21005, 21004]
Abstract: Vaccine development against the SARS-CoV-2 virus focuses on the principal target of the neutralizing immune response, the spike (S) glycoprotein. Adenovirus-vectored vaccines offer an effective platform for the delivery of viral antigen, but it is important for the generation of neutralizing antibodies that they produce appropriately processed and assembled viral antigen that mimics that observed on the SARS-CoV-2 virus. Here, we describe the structure, conformation, and glycosylation of the S protein derived from the adenovirus-vectored ChAdOx1 nCoV-19/AZD1222 vaccine. We demonstrate native-like post-translational processing and assembly, and reveal the expression of S proteins on the surface of cells adopting the trimeric prefusion conformation. The data presented here confirm the use of ChAdOx1 adenovirus vectors as a leading platform technology for SARS-CoV-2 vaccines.
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Apr 2021
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Sebastian
Gunther
,
Patrick Y. A.
Reinke
,
Yaiza
Fernández-García
,
Julia
Lieske
,
Thomas J.
Lane
,
Helen M.
Ginn
,
Faisal H. M.
Koua
,
Christiane
Ehrt
,
Wiebke
Ewert
,
Dominik
Oberthuer
,
Oleksandr
Yefanov
,
Susanne
Meier
,
Kristina
Lorenzen
,
Boris
Krichel
,
Janine-Denise
Kopicki
,
Luca
Gelisio
,
Wolfgang
Brehm
,
Ilona
Dunkel
,
Brandon
Seychell
,
Henry
Gieseler
,
Brenna
Norton-Baker
,
Beatriz
Escudero-Pérez
,
Martin
Domaracky
,
Sofiane
Saouane
,
Alexandra
Tolstikova
,
Thomas A.
White
,
Anna
Hänle
,
Michael
Groessler
,
Holger
Fleckenstein
,
Fabian
Trost
,
Marina
Galchenkova
,
Yaroslav
Gevorkov
,
Chufeng
Li
,
Salah
Awel
,
Ariana
Peck
,
Miriam
Barthelmess
,
Frank
Schluenzen
,
Paulraj
Lourdu Xavier
,
Nadine
Werner
,
Hina
Andaleeb
,
Najeeb
Ullah
,
Sven
Falke
,
Vasundara
Srinivasan
,
Bruno Alves
França
,
Martin
Schwinzer
,
Hévila
Brognaro
,
Cromarte
Rogers
,
Diogo
Melo
,
Joanna J.
Zaitseva-Doyle
,
Juraj
Knoska
,
Gisel E.
Peña-Murillo
,
Aida Rahmani
Mashhour
,
Vincent
Hennicke
,
Pontus
Fischer
,
Johanna
Hakanpää
,
Jan
Meyer
,
Philip
Gribbon
,
Bernhard
Ellinger
,
Maria
Kuzikov
,
Markus
Wolf
,
Andrea R.
Beccari
,
Gleb
Bourenkov
,
David
Von Stetten
,
Guillaume
Pompidor
,
Isabel
Bento
,
Saravanan
Panneerselvam
,
Ivars
Karpics
,
Thomas R.
Schneider
,
Maria Marta
Garcia-Alai
,
Stephan
Niebling
,
Christian
Günther
,
Christina
Schmidt
,
Robin
Schubert
,
Huijong
Han
,
Juliane
Boger
,
Diana C. F.
Monteiro
,
Linlin
Zhang
,
Xinyuanyuan
Sun
,
Jonathan
Pletzer-Zelgert
,
Jan
Wollenhaupt
,
Christian G.
Feiler
,
Manfred S.
Weiss
,
Eike-Christian
Schulz
,
Pedram
Mehrabi
,
Katarina
Karničar
,
Aleksandra
Usenik
,
Jure
Loboda
,
Henning
Tidow
,
Ashwin
Chari
,
Rolf
Hilgenfeld
,
Charlotte
Uetrecht
,
Russell
Cox
,
Andrea
Zaliani
,
Tobias
Beck
,
Matthias
Rarey
,
Stephan
Günther
,
Dusan
Turk
,
Winfried
Hinrichs
,
Henry N.
Chapman
,
Arwen R.
Pearson
,
Christian
Betzel
,
Alke
Meents
Open Access
Abstract: The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and six non-peptidic compounds showed antiviral activity at non-toxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.
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Apr 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Sergio
Celis
,
Fruzsina
Hobor
,
Thomas
James
,
Gail J.
Bartlett
,
Amaurys A.
Ibarra
,
Deborah K.
Shoemark
,
Zsofia
Hegedus
,
Kristina
Hetherington
,
Derek N.
Woolfson
,
Richard B.
Sessions
,
Thomas A.
Edwards
,
David M.
Andrews
,
Adam
Nelson
,
Andrew J.
Wilson
Diamond Proposal Number(s):
[19248]
Open Access
Abstract: Protein–protein interactions (PPIs) are central to biological mechanisms, and can serve as compelling targets for drug discovery. Yet, the discovery of small molecule inhibitors of PPIs remains challenging given the large and typically shallow topography of the interacting protein surfaces. Here, we describe a general approach to the discovery of orthosteric PPI inhibitors that mimic specific secondary protein structures. Initially, hot residues at protein–protein interfaces are identified in silico or from experimental data, and incorporated into secondary structure-based queries. Virtual libraries of small molecules are then shape-matched against the queries, and promising ligands docked to target proteins. The approach is exemplified experimentally using two unrelated PPIs that are mediated by an α-helix (p53/hDM2) and a β-strand (GKAP/SHANK1-PDZ). In each case, selective PPI inhibitors are discovered with low μM activity as determined by a combination of fluorescence anisotropy and 1H–15N HSQC experiments. In addition, hit expansion yields a series of PPI inhibitors with defined structure–activity relationships. It is envisaged that the generality of the approach will enable discovery of inhibitors of a wide range of unrelated secondary structure-mediated PPIs.
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Mar 2021
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I05-ARPES
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Paulina
Majchrzak
,
Ryan
Muzzio
,
Alfred J. H.
Jones
,
Davide
Curcio
,
Klara
Volckaert
,
Deepnarayan
Biswas
,
Jacob
Gobbo
,
Simranjeet
Singh
,
Jeremy T.
Robinson
,
Kenji
Watanabe
,
Takashi
Taniguchi
,
Timur K.
Kim
,
Cephise
Cacho
,
Jill A.
Miwa
,
Philip
Hofmann
,
Jyoti
Katoch
,
Soeren
Ulstrup
Diamond Proposal Number(s):
[24072]
Open Access
Abstract: To pinpoint the electronic and structural mechanisms that affect intrinsic and extrinsic performance limits of two‐dimensional material devices, it is of critical importance to resolve the electronic properties on the mesoscopic length scale of such devices under operating conditions. The present work utilizes angle‐resolved photoemission spectroscopy with nanoscale spatial resolution (nanoARPES) to map the quasiparticle electronic structure of a twisted bilayer graphene device. The dispersion and linewidth of the Dirac cones associated with top and bottom graphene layers are determined as a function of spatial position on the device under both static and operating conditions. The analysis reveals that microscopic rotational domains in the two graphene layers establish a range of twist angles from 9.8∘ to 12.7∘. Application of current and electrostatic gating lead to strong electric fields with peak strengths of 0.75 V/μm at the rotational domain boundaries in the device. These proof‐of‐principle results demonstrate the potential of nanoARPES to link mesoscale structural variations with electronic states in operating device conditions and to disentangle such extrinsic factors from the intrinsic quasiparticle dispersion.
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Mar 2021
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I19-Small Molecule Single Crystal Diffraction
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Aaron J
Scott
,
Euan K.
Brechin
,
Stergios
Piligkos
,
Gopalan
Rajaraman
,
Mark
Murrie
,
Simon
Coles
,
Wim T.
Klooster
,
Gary S.
Nichol
,
Paul
Lusby
,
Lucy
Smythe
,
Arup
Sarkar
,
Julia
Vallejo
,
Emma
Regincos Marti
Diamond Proposal Number(s):
[22240]
Open Access
Abstract: Reaction of Ni(OTf)2 with the bisbidentate quaterpyridine ligand L results in the self-assembly of a tetrahedral, paramagnetic cage [NiII4L6]8+. By selectively exchanging the bound triflate from [OTf⊂NiII4L6](OTf)7 (1), we have been able to prepare a series of host-guest complexes that feauture an encapsulated paramagnetic tetrahalometallate ion inside this paramagnetic host giving [MIIX4⊂NiII4L6](OTf)6, where MIIX42− = MnCl42− (2), CoCl42− (5), CoBr42− (6), NiCl42− (7), CuBr42− (8) or [MIIIX4⊂NiII4L6](OTf)7, where MIIIX4− = FeCl4− (3), FeBr4− (4). Triflate-to-tetrahalometallate exchange occurs in solution and can also be accomplished through single-crystal-to-single-crystal transformations. Host-guest complexes 1-8 all crystallise as homochiral racemates in monoclinic space groups, wherein the four {NiN6} vertex within a single Ni4L6 unit possess the same Δ or Λ stereochemistry. Magnetic susceptibility and magnetisation data show that the magnetic exchange between metal ions in the host [NiII4] complex, and between the host and the MX4n- guest, are of comparable magnitude and antiferromagnetic in nature. Theoretically derived values for the magnetic exchange are in close agreement with experiment, revealing that large spin densities on the electronegative X-atoms of particular {MX4}n− guest molecules leads to stronger host-guest magnetic exchange interactions.
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Mar 2021
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B18-Core EXAFS
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Diamond Proposal Number(s):
[12767, 13599]
Abstract: Geological disposal is the globally preferred long-term solution for higher activity radioactive wastes (HAW) including intermediate level waste (ILW). In a cementitious disposal system, cellulosic waste items present in ILW may undergo alkaline hydrolysis, producing significant quantities of isosaccharinic acid (ISA), a chelating agent for radionuclides. Although microbial degradation of ISA has been demonstrated, its impact upon the fate of radionuclides in a geological disposal facility (GDF) is a topic of ongoing research. This study investigates the fate of U(VI) in pH-neutral, anoxic, microbial enrichment cultures, approaching conditions similar to the far field of a GDF, containing ISA as the sole carbon source, and elevated phosphate concentrations, incubated both (i) under fermentation and (ii) Fe(III)-reducing conditions. In the ISA-fermentation experiment, U(VI) was precipitated as insoluble U(VI)-phosphates, whereas under Fe(III)-reducing conditions, the majority of the uranium was precipitated as reduced U(IV)-phosphates, presumably formed via enzymatic reduction mediated by metal-reducing bacteria, including Geobacter species. Overall, this suggests the establishment of a microbially mediated “bio-barrier” extending into the far field geosphere surrounding a GDF is possible and this biobarrier has the potential to evolve in response to GDF evolution and can have a controlling impact on the fate of radionuclides.
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Mar 2021
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Husam Sabah
Auhim
,
Bella L.
Grigorenko
,
Tessa K.
Harris
,
Ozan E.
Aksakal
,
Igor V.
Polyakov
,
Colin
Berry
,
Gabriel Dos Passos
Gomes
,
Igor V.
Alabugin
,
Pierre J.
Rizkallah
,
Alexander V.
Nemukhin
,
D. Dafydd
Jones
Diamond Proposal Number(s):
[18812]
Open Access
Abstract: Fluorescent proteins (FPs) have revolutionised the life sciences, but the mechanism of chromophore maturation is still not fully understood. Here we show that incorporation of a photo-responsive non-canonical amino acid within the chromophore stalls maturation of Venus, a yellow FP, at an intermediate stage; a crystal structure indicates the presence of O2 located above a dehydrated enolate form of the imidazolone ring, close to the strictly conserved Gly67 that occupies a twisted conformation. His148 adopts an “open” conformation so forming a channel that allows O2 access to the immature chromophore. Absorbance spectroscopy supported by QM/MM simulations suggests that the first oxidation step involves formation of a hydroperoxyl intermediate in conjunction with dehydrogenation of the methylene bridge. A fully conjugated mature chromophore is formed through release of H2O2, both in vitro and in vivo. The possibility of interrupting and photochemically restarting chromophore maturation and the mechanistic insights open up new approaches for engineering optically controlled fluorescent proteins.
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Mar 2021
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P.
Mehrabi
,
R.
Bücker
,
G.
Bourenkov
,
H. M.
Ginn
,
D.
Von Stetten
,
H. M.
Müller-Werkmeister
,
A.
Kuo
,
T.
Morizumi
,
B.t.
Eger
,
W.-L.
Ou
,
S.
Oghbaey
,
A.
Sarracini
,
J. E.
Besaw
,
O.
Pare´-Labrosse
,
S.
Meier
,
H.
Schikora
,
F.
Tellkamp
,
A.
Marx
,
D. A.
Sherrell
,
D.
Axford
,
R. I.
Owen
,
O. P.
Ernst
,
E. F.
Pai
,
E. C.
Schulz
,
R. J. D.
Miller
Open Access
Abstract: For the two proteins myoglobin and fluoroacetate dehalogenase, we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of micron-sized crystals, the same sample delivery device, and the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins, reasonable data statistics can be obtained with approximately 5000 room-temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that the quality of diffraction data obtained from these samples is linked to the properties of the crystals rather than to the radiation source. Therefore, for other systems with similar properties, time-resolved experiments can be conducted at the radiation source that best matches the desired time resolution.
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Mar 2021
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[15444]
Abstract: Inorganic/organic hybrids have co-networks of inorganic and organic components, with the aim of obtaining synergy of the properties of those components. Here, a silica-gelatin sol-gel hybrid “ink” was directly 3D printed to produce 3D grid-like scaffolds, using a coupling agent, 3-glycidyloxypropyl)trimethoxysilane (GPTMS), to form covalent bonds between the silicate and gelatin co-networks. Scaffolds were printed with 1 mm strut separation, but the drying method affected the final architecture and properties. Freeze drying produced <40 μm struts and large ~700 μm channels. Critical point drying enabled strut consolidation and optimal mechanical properties, with ~160 μm struts and ~200 μm channels, which improved mechanical properties. This architecture was critical to cellular response: when chondrocytes were seeded on the scaffolds with 200 μm wide pore channels in vitro, collagen Type II matrix was preferentially produced (negligible amount of Type I or X were observed), indicative of hyaline-like cartilaginous matrix formation, but when pore channels were 700 μm wide, Type I collagen was prevalent. This was supported by Sox9 and Aggrecan expression. The scaffolds have potential for regeneration of articular cartilage regeneration, particularly in sports medicine cases.
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Feb 2021
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