I07-Surface & interface diffraction
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Diamond Proposal Number(s):
[18591]
Open Access
Abstract: The adsorption of carboxylic acid molecules at the calcite (104) and the muscovite (001) surface was investigated using surface X-ray diffraction. All four investigated carboxylic acid molecules, hexanoic acid, octanoic acid, lauric acid, and stearic acid, were found to adsorb at the calcite surface. Whereas the shortest two carboxylic acid molecules, hexanoic acid and octanoic acid, showed limited ordering and a flexible, disordered chain, the two longest carboxylic acid molecules form fully ordered monolayers, i.e., these form highly structured self-assembled monolayers. The latter molecules are oriented almost fully upright, with a tilt of up to 10°. The oxygen atoms of the organic molecules are found at similar positions to those of water molecules at the calcite–water interface. This suggests that in both cases, the oxygen atoms compensate for the broken bonds at the calcite surface. Under the same experimental conditions, stearic acid does not adsorb to K+ and Ca2+-functionalized muscovite mica because the neutral molecules do not engage in the ionic bonds typical for the mica interface. These differences in adsorption behavior are characteristic for the differences of the oil–solid interactions in carbonate and sandstone reservoirs.
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May 2022
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I03-Macromolecular Crystallography
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Nikolaos
Georgakopoulos
,
Sandeep
Talapatra
,
Dina
Dikovskaya
,
Sharadha
Dayalan Naidu
,
Maureen
Higgins
,
Jemma
Gatliff
,
Aysel
Ayhan
,
Roxani
Nikoloudaki
,
Marjolein
Schaap
,
Klara
Valko
,
Farideh
Javid
,
Albena T.
Dinkova-Kostova
,
Frank
Kozielski
,
Geoffrey
Wells
Diamond Proposal Number(s):
[12305]
Open Access
Abstract: Inhibitors of Kelch-like ECH-associated protein 1 (Keap1) increase the activity of the transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2) by stalling its ubiquitination and degradation. This enhances the expression of genes encoding proteins involved in drug detoxification, redox homeostasis, and mitochondrial function. Nrf2 activation offers a potential therapeutic approach for conditions including Alzheimer’s and Parkinson’s diseases, vascular inflammation, and chronic obstructive airway disease. Non-electrophilic Keap1-Nrf2 protein–protein interaction (PPI) inhibitors may have improved toxicity profiles and different pharmacological properties to cysteine-reactive electrophilic inhibitors. Here, we describe and characterize a series of phenyl bis-sulfonamide PPI inhibitors that bind to Keap1 at submicromolar concentrations. Structural studies reveal that the compounds bind to Keap1 in a distinct “peptidomimetic” conformation that resembles the Keap1-Nrf2 ETGE peptide complex. This is different to other small molecule Keap1-Nrf2 PPI inhibitors, including bicyclic aryl bis-sulfonamides, offering a starting point for new design approaches to Keap1 inhibitors.
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May 2022
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B24-Cryo Soft X-ray Tomography
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Diamond Proposal Number(s):
[18925, 19958, 21485, 23508]
Open Access
Abstract: Cryo-soft-X-ray tomography is being increasingly used in biological research to study the morphology of cellular compartments and how they change in response to different stimuli, such as viral infections. Segmentation of these compartments is limited by time-consuming manual tools or machine learning algorithms that require extensive time and effort to train. Here we describe Contour, a new, easy-to-use, highly automated segmentation tool that enables accelerated segmentation of tomograms to delineate distinct cellular compartments. Using Contour, cellular structures can be segmented based on their projection intensity and geometrical width by applying a threshold range to the image and excluding noise smaller in width than the cellular compartments of interest. This method is less laborious and less prone to errors from human judgement than current tools that require features to be manually traced, and it does not require training datasets as would machine-learning driven segmentation. We show that high-contrast compartments such as mitochondria, lipid droplets, and features at the cell surface can be easily segmented with this technique in the context of investigating herpes simplex virus 1 infection. Contour can extract geometric measurements from 3D segmented volumes, providing a new method to quantitate cryo-soft-X-ray tomography data. Contour can be freely downloaded at github.com/kamallouisnahas/Contour.
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May 2022
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Nicky J.
Willis
,
William
Mahy
,
James
Sipthorp
,
Yuguang
Zhao
,
Hannah L.
Woodward
,
Benjamin N.
Atkinson
,
Elliott D.
Bayle
,
Fredrik
Svensson
,
Sarah
Frew
,
Fiona
Jeganathan
,
Amy
Monaghan
,
Stefano
Benvegnù
,
Sarah
Jolly
,
Luca
Vecchia
,
Reinis R.
Ruza
,
Svend
Kjær
,
Steven
Howell
,
Ambrosius P.
Snijders
,
Magda
Bictash
,
Patricia C.
Salinas
,
Jean-Paul
Vincent
,
E. Yvonne
Jones
,
Paul
Whiting
,
Paul V.
Fish
Diamond Proposal Number(s):
[16814, 19446]
Open Access
Abstract: Notum is a carboxylesterase that suppresses Wnt signaling through deacylation of an essential palmitoleate group on Wnt proteins. There is a growing understanding of the role Notum plays in human diseases such as colorectal cancer and Alzheimer’s disease, supporting the need to discover improved inhibitors, especially for use in models of neurodegeneration. Here, we have described the discovery and profile of 8l (ARUK3001185) as a potent, selective, and brain-penetrant inhibitor of Notum activity suitable for oral dosing in rodent models of disease. Crystallographic fragment screening of the Diamond-SGC Poised Library for binding to Notum, supported by a biochemical enzyme assay to rank inhibition activity, identified 6a and 6b as a pair of outstanding hits. Fragment development of 6 delivered 8l that restored Wnt signaling in the presence of Notum in a cell-based reporter assay. Assessment in pharmacology screens showed 8l to be selective against serine hydrolases, kinases, and drug targets.
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May 2022
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I07-Surface & interface diffraction
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Diamond Proposal Number(s):
[20529]
Abstract: We present a surface-sensitive X-ray scattering study on the influence of gaseous and aerolized perfluorocarbons (FCs) on zwitterionic and anionic phospholipid Langmuir films, which serve as a simplified model system of lung surfactants. It was found that small gaseous FC molecules like F-propane and F-butane penetrate phospholipid monolayers and accumulate between the alkyl chains and form islands. This clustering process can trigger the formation of lipid crystallites at low initial surface pressures. In contrast, the large linear FC F-octyl bromide fluidizes membranes, causing a dissolution of crystalline domains. The bicyclic FC F-decalin accumulates between the alkyl chains of 1,2-dipalmitoyl phosphatidylcholine but cannot penetrate the more densely packed 1,2-dipalmitoyl phosphatidic acid films because of its size. The effects of FCs on lung surfactants are discussed in the framework of currently proposed therapeutic methods for acute respiratory distress syndrome using FC gases, vapor, or aerosol ventilation causing monolayer fluidization effects. This study implies that the highly biocompatible and nontoxic FCs could be beneficial in the treatment of lung diseases with injured nonfunctional lung surfactants in a novel approach for ventilation.
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May 2022
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I14-Hard X-ray Nanoprobe
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Diamond Proposal Number(s):
[22977]
Open Access
Abstract: Background: Established MRI and emerging X-ray contrast agents for non-invasive imaging of articular cartilage rely on non-selective electrostatic interactions with negatively charged proteoglycans. These contrast agents have limited prognostic utility in diseases such as osteoarthritis (OA) due to the characteristic high turnover of proteoglycans. To overcome this limitation, we developed a radiocontrast agent that targets the type II collagen macromolecule in cartilage and used it to monitor disease progression in a murine model of OA. Methods: To confer radiopacity to cartilage contrast agents, the naturally occurring tyrosine derivative 3,5-diiodo-L-tyrosine (DIT) was introduced into a selective peptide for type II collagen. Synthetic DIT peptide derivatives were synthesised by Fmoc-based solid-phase peptide synthesis and binding to ex vivo mouse tibial cartilage evaluated by high-resolution micro-CT. Di-Iodotyrosinated Peptide Imaging of Cartilage (DIPIC) was performed ex vivo and in vivo 4, 8 and 12 weeks in mice after induction of OA by destabilisation of the medial meniscus (DMM). Finally, human osteochondral plugs were imaged ex vivo using DIPIC. Results: Fifteen DIT peptides were synthesised and tested, yielding seven leads with varying cartilage binding strengths. DIPIC visualised ex vivo murine articular cartilage comparably to the ex vivo contrast agent phosphotungstic acid. Intra-articular injection of contrast agent followed by in vivo DIPIC enabled delineation of damaged murine articular cartilage. Finally, the translational potential of the contrast agent was confirmed by visualisation of ex vivo human cartilage explants. Conclusion: DIPIC has reduction and refinement implications in OA animal research and potential clinical translation to imaging human disease.
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May 2022
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[20145]
Abstract: During the initiation of DNA replication, oligonucleotide primers are synthesized de novo by primases and are subsequently extended by replicative polymerases to complete genome duplication. The primase-polymerase (Prim-Pol) superfamily is a diverse grouping of primases, which includes replicative primases and CRISPR-associated primase-polymerases (CAPPs) involved in adaptive immunity1,2,3. Although much is known about the activities of these enzymes, the precise mechanism used by primases to initiate primer synthesis has not been elucidated. Here we identify the molecular bases for the initiation of primer synthesis by CAPP and show that this mechanism is also conserved in replicative primases. The crystal structure of a primer initiation complex reveals how the incoming nucleotides are positioned within the active site, adjacent to metal cofactors and paired to the templating single-stranded DNA strand, before synthesis of the first phosphodiester bond. Furthermore, the structure of a Prim-Pol complex with double-stranded DNA shows how the enzyme subsequently extends primers in a processive polymerase mode. The structural and mechanistic studies presented here establish how Prim-Pol proteins instigate primer synthesis, revealing the requisite molecular determinants for primer synthesis within the catalytic domain. This work also establishes that the catalytic domain of Prim-Pol enzymes, including replicative primases, is sufficient to catalyse primer formation.
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May 2022
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I11-High Resolution Powder Diffraction
I15-Extreme Conditions
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Diamond Proposal Number(s):
[14061, 17673, 16390]
Open Access
Abstract: The similar electronic structures of Bi3+ and Pb2+ have motivated researchers to explore bismuth-based perovskite compounds, which in the past decade has been further fuelled by the demand for developing lead-free piezoceramics. The difficulty in stabilizing the perovskite phase in bismuth based compounds has directed most research activities towards exploring two main compounds - multiferroic BiFeO3 and relaxor ferroelectric Na1/2Bi1/2TiO3 and their derivatives. In recent years, quenching these materials from the sintering temperature or from the paraelectric phase (above the Curie temperature, Tc) has resulted in a plethora of fundamentally interesting and technologically relevant advances, including enhanced thermal depolarization temperature, high Tc, giant strain and control over the atomic structure and electrical conductivity at the domain wall. In this contribution, a brief overview of quenching piezoceramics is presented, with majority of the discussion encompassing salient features of quenching lead-free perovskite structured Na1/2Bi1/2TiO3- and BiFeO3- based materials. For each material system, the influence of quenching on phase transitions, domain switching behavior and electromechanical properties are presented, apart from outlining the current understanding of the underlying mechanisms. The review provides guidelines for further exploration of the quenching strategy for improving the functionality of Bi-based piezoceramics.
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May 2022
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Krios I-Titan Krios I at Diamond
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Diamond Proposal Number(s):
[2154]
Abstract: Human α2-macroglobulin (hα2M) is a multidomain protein with a plethora of essential functions, including transport of signaling molecules and endopeptidase inhibition in innate immunity. Here, we dissected the molecular mechanism of the inhibitory function of the ∼720-kDa hα2M tetramer through eight cryo–electron microscopy (cryo-EM) structures of complexes from human plasma. In the native complex, the hα2M subunits are organized in two flexible modules in expanded conformation, which enclose a highly porous cavity in which the proteolytic activity of circulating plasma proteins is tested. Cleavage of bait regions exposed inside the cavity triggers rearrangement to a compact conformation, which closes openings and entraps the prey proteinase. After the expanded-to-compact transition, which occurs independently in the four subunits, the reactive thioester bond triggers covalent linking of the proteinase, and the receptor-binding domain is exposed on the tetramer surface for receptor-mediated clearance from circulation. These results depict the molecular mechanism of a unique suicidal inhibitory trap.
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May 2022
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[26802]
Open Access
Abstract: Herein we disclose a mild protocol for the reductive functionalisation of quinolinium and isoquinolinium salts. The reaction proceeds under transition-metal-free conditions as well as under rhodium catalysis with very low catalyst loadings (0.01 mol %) and uses inexpensive formic acid as the terminal reductant. A wide range of electrophiles, including enones, imides, unsaturated esters and sulfones, β-nitro styrenes and aldehydes are intercepted by the in situ formed enamine species forming a large variety of substituted tetrahydro(iso)quinolines. Electrophiles are incorporated at the C-3 and C-4 position for quinolines and isoquinolines respectively, providing access to substitution patterns which are not favoured in electrophilic or nucleophilic aromatic substitution. Finally, this reactivity was exploited to facilitate three types of annulation reactions, giving rise to complex polycyclic products of a formal [3+3] or [4+2] cycloaddition.
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May 2022
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