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295 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3, 4, 5, 6, 7, 8 [Next/Last]

Instruments / Technical Area	Publication Details	Published
B18-Core EXAFS	Cation insertion to break the activity/stability relationship for highly active oxygen evolution reaction catalyst Chunzhen Yang , Gwenaëlle Rousse , Katrine Louise Svane , Paul E. Pearce , Artem M. Abakumov , Michael Deschamps , Giannantonio Cibin , Alan V. Chadwick , Daniel Alves Dalla Corte , Heine Anton Hansen , Tejs Vegge , Jean-marie Tarascon , Alexis Grimaud Nature Communications 11 DOI: 10.1038/s41467-020-15231-x Diamond Proposal Number(s): [14239] Open Access Show Abstract ▼ Abstract: The production of hydrogen at a large scale by the environmentally-friendly electrolysis process is currently hampered by the slow kinetics of the oxygen evolution reaction (OER). We report a solid electrocatalyst α-Li2IrO3 which upon oxidation/delithiation chemically reacts with water to form a hydrated birnessite phase, the OER activity of which is five times greater than its non-reacted counterpart. This reaction enlists a bulk redox process during which hydrated potassium ions from the alkaline electrolyte are inserted into the structure while water is oxidized and oxygen evolved. This singular charge balance process for which the electrocatalyst is solid but the reaction is homogeneous in nature allows stabilizing the surface of the catalyst while ensuring stable OER performances, thus breaking the activity/stability tradeoff normally encountered for OER catalysts.	Mar 2020
I03-Macromolecular Crystallography	A receptor for the complement regulator factor H increases transmission of trypanosomes to tsetse flies Olivia J. S. Macleod , Jean-mathieu Bart , Paula Macgregor , Lori Peacock , Nicholas J. Savill , Svenja Hester , Sophie Ravel , Jack D. Sunter , Camilla Trevor , Steven Rust , Tristan J. Vaughan , Ralph Minter , Shabaz Mohammed , Wendy Gibson , Martin C. Taylor , Matthew Higgins , Mark Carrington Nature Communications 11 DOI: 10.1038/s41467-020-15125-y Diamond Proposal Number(s): [18069] Open Access Show Abstract ▼ Abstract: Persistent pathogens have evolved to avoid elimination by the mammalian immune system including mechanisms to evade complement. Infections with African trypanosomes can persist for years and cause human and animal disease throughout sub-Saharan Africa. It is not known how trypanosomes limit the action of the alternative complement pathway. Here we identify an African trypanosome receptor for mammalian factor H, a negative regulator of the alternative pathway. Structural studies show how the receptor binds ligand, leaving inhibitory domains of factor H free to inactivate complement C3b deposited on the trypanosome surface. Receptor expression is highest in developmental stages transmitted to the tsetse fly vector and those exposed to blood meals in the tsetse gut. Receptor gene deletion reduced tsetse infection, identifying this receptor as a virulence factor for transmission. This demonstrates how a pathogen evolved a molecular mechanism to increase transmission to an insect vector by exploitation of a mammalian complement regulator.	Mar 2020
I04-Macromolecular Crystallography	Revisiting the pH-gated conformational switch on the activities of HisKA-family histidine kinases Maria Cristina Mideros-mora , Laura Miguel-romero , Alonso Felipe-ruiz , Patricia Casino , Alberto Marina Nature Communications 11 DOI: 10.1038/s41467-020-14540-5 Diamond Proposal Number(s): [14739, 20229] Open Access Show Abstract ▼ Abstract: Histidine is a versatile residue playing key roles in enzyme catalysis thanks to the chemistry of its imidazole group that can serve as nucleophile, general acid or base depending on its protonation state. In bacteria, signal transduction relies on two-component systems (TCS) which comprise a sensor histidine kinase (HK) containing a phosphorylatable catalytic His with phosphotransfer and phosphatase activities over an effector response regulator. Recently, a pH-gated model has been postulated to regulate the phosphatase activity of HisKA HKs based on the pH-dependent rotamer switch of the phosphorylatable His. Here, we have revisited this model from a structural and functional perspective on HK853–RR468 and EnvZ–OmpR TCS, the prototypical HisKA HKs. We have found that the rotamer of His is not influenced by the environmental pH, ruling out a pH-gated model and confirming that the chemistry of the His is responsible for the decrease in the phosphatase activity at acidic pH.	Feb 2020
I24-Microfocus Macromolecular Crystallography	Structural basis for substrate specificity and catalysis of α1,6-fucosyltransferase Ana García-garcía , Laura Ceballos-laita , Sonia Serna , Raik Artschwager , Niels C. Reichardt , Francisco Corzana , Ramon Hurtado-guerrero Nature Communications 11 DOI: 10.1038/s41467-020-14794-z Diamond Proposal Number(s): [20229] Open Access Show Abstract ▼ Abstract: Core-fucosylation is an essential biological modification by which a fucose is transferred from GDP-β-L-fucose to the innermost N-acetylglucosamine residue of N-linked glycans. A single human enzyme α1,6-fucosyltransferase (FUT8) is the only enzyme responsible for this modification via the addition of an α-1,6-linked fucose to N-glycans. To date, the details of substrate recognition and catalysis by FUT8 remain unknown. Here, we report the crystal structure of FUT8 complexed with GDP and a biantennary complex N-glycan (G0), which provides insight into both substrate recognition and catalysis. FUT8 follows an SN2 mechanism and deploys a series of loops and an α-helix which all contribute in forming the binding site. An exosite, formed by one of these loops and an SH3 domain, is responsible for the recognition of branched sugars, making contacts specifically to the α1,3 arm GlcNAc, a feature required for catalysis. This information serves as a framework for inhibitor design, and helps to assess its potential as a therapeutic target.	Feb 2020
I03-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Structural basis of mammalian high-mannose N-glycan processing by human gut Bacteroides Beatriz Trastoy , Jonathan J. Du , Erik H. Klontz , Chao Li , Javier O. Cifuente , Lai-xi Wang , Eric J. Sundberg , Marcelo E. Guerin Nature Communications 11 DOI: 10.1038/s41467-020-14754-7 Diamond Proposal Number(s): [20113] Open Access Show Abstract ▼ Abstract: The human gut microbiota plays a central role not only in regulating the metabolism of nutrients but also promoting immune homeostasis, immune responses and protection against pathogen colonization. The genome of the Gram-negative symbiont Bacteroides thetaiotaomicron, a dominant member of the human intestinal microbiota, encodes polysaccharide utilization loci PULs, the apparatus required to orchestrate the degradation of a specific glycan. EndoBT-3987 is a key endo-β-N-acetylglucosaminidase (ENGase) that initiates the degradation/processing of mammalian high-mannose-type (HM-type) N-glycans in the intestine. Here, we provide structural snapshots of EndoBT-3987, including the unliganded form, the EndoBT-3987-Man9GlcNAc2Asn substrate complex, and two EndoBT-3987-Man9GlcNAc and EndoBT-3987-Man5GlcNAc product complexes. In combination with alanine scanning mutagenesis and activity measurements we unveil the molecular mechanism of HM-type recognition and specificity for EndoBT-3987 and an important group of the GH18 ENGases, including EndoH, an enzyme extensively used in biotechnology, and for which the mechanism of substrate recognition was largely unknown.	Feb 2020
Krios IV-Titan Krios IV at Diamond	Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain Alister Burt , C. Keith Cassidy , Peter Ames , Maria Bacia-verloop , Megghane Baulard , Karine Huard , Zaida Luthey-schulten , Ambroise Desfosses , Phillip J. Stansfeld , William Margolin , John S. Parkinson , Irina Gutsche Nature Communications 11 DOI: 10.1038/s41467-020-14350-9 Diamond Proposal Number(s): [18112] Open Access Show Abstract ▼ Abstract: Motile bacteria sense chemical gradients with transmembrane receptors organised in supramolecular signalling arrays. Understanding stimulus detection and transmission at the molecular level requires precise structural characterisation of the array building block known as a core signalling unit. Here we introduce an Escherichia coli strain that forms small minicells possessing extended and highly ordered chemosensory arrays. We use cryo-electron tomography and subtomogram averaging to provide a three-dimensional map of a complete core signalling unit, with visible densities corresponding to the HAMP and periplasmic domains. This map, combined with previously determined high resolution structures and molecular dynamics simulations, yields a molecular model of the transmembrane core signalling unit and enables spatial localisation of its individual domains. Our work thus offers a solid structural basis for the interpretation of a wide range of existing data and the design of further experiments to elucidate signalling mechanisms within the core signalling unit and larger array.	Feb 2020
	Hand-foot-and-mouth disease virus receptor KREMEN1 binds the canyon of Coxsackie Virus A10 Yuguang Zhao , Daming Zhou , Tao Ni , Dimple Karia , Abhay Kotecha , Xiangxi Wang , Zihe Rao , E. Yvonne Jones , Elizabeth E. Fry , Jingshan Ren , David I. Stuart Nature Communications 11 DOI: 10.1038/s41467-019-13936-2 Open Access Show Abstract ▼ Abstract: Coxsackievirus A10 (CV-A10) is responsible for an escalating number of severe infections in children, but no prophylactics or therapeutics are currently available. KREMEN1 (KRM1) is the entry receptor for the largest receptor-group of hand-foot-and-mouth disease causing viruses, which includes CV-A10. We report here structures of CV-A10 mature virus alone and in complex with KRM1 as well as of the CV-A10 A-particle. The receptor spans the viral canyon with a large footprint on the virus surface. The footprint has some overlap with that seen for the neonatal Fc receptor complexed with enterovirus E6 but is larger and distinct from that of another enterovirus receptor SCARB2. Reduced occupancy of a particle-stabilising pocket factor in the complexed virus and the presence of both unbound and expanded virus particles suggests receptor binding initiates a cascade of conformational changes that produces expanded particles primed for viral uncoating.	Jan 2020
I24-Microfocus Macromolecular Crystallography	Structures of lipoprotein signal peptidase II from Staphylococcus aureus complexed with antibiotics globomycin and myxovirescin Samir Olatunji , Xiaoxiao Yu , Jonathan Bailey , Chia-ying Huang , Marta Zapotoczna , Katherine Bowen , Maja Remškar , Rolf Müller , Eoin M. Scanlan , Joan A. Geoghegan , Vincent Olieric , Martin Caffrey Nature Communications 11 DOI: 10.1038/s41467-019-13724-y Diamond Proposal Number(s): [17810] Open Access Show Abstract ▼ Abstract: Antimicrobial resistance is a major global threat that calls for new antibiotics. Globomycin and myxovirescin are two natural antibiotics that target the lipoprotein-processing enzyme, LspA, thereby compromising the integrity of the bacterial cell envelope. As part of a project aimed at understanding their mechanism of action and for drug development, we provide high-resolution crystal structures of the enzyme from the human pathogen methicillin-resistant Staphylococcus aureus (MRSA) complexed with globomycin and with myxovirescin. Our results reveal an instance of convergent evolution. The two antibiotics possess different molecular structures. Yet, they appear to inhibit identically as non-cleavable tetrahedral intermediate analogs. Remarkably, the two antibiotics superpose along nineteen contiguous atoms that interact similarly with LspA. This 19-atom motif recapitulates a part of the substrate lipoprotein in its proposed binding mode. Incorporating this motif into a scaffold with suitable pharmacokinetic properties should enable the development of effective antibiotics with built-in resistance hardiness.	Jan 2020
B21-High Throughput SAXS	Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution Doo Nam Kim , Bernhard C. Thiel , Tyler Mrozowich , Scott P. Hennelly , Ivo L. Hofacker , Trushar R. Patel , Karissa Y. Sanbonmatsu Nature Communications 11 DOI: 10.1038/s41467-019-13942-4 Diamond Proposal Number(s): [16028] Open Access Show Abstract ▼ Abstract: Long non-coding RNAs (lncRNAs) constitute a significant fraction of the transcriptome, playing important roles in development and disease. However, our understanding of structure-function relationships for this emerging class of RNAs has been limited to secondary structures. Here, we report the 3-D atomistic structural study of epigenetic lncRNA, Braveheart (Bvht), and its complex with CNBP (Cellular Nucleic acid Binding Protein). Using small angle X-ray scattering (SAXS), we elucidate the ensemble of Bvht RNA conformations in solution, revealing that Bvht lncRNA has a well-defined, albeit flexible 3-D structure that is remodeled upon CNBP binding. Our study suggests that CNBP binding requires multiple domains of Bvht and the RHT/AGIL RNA motif. We show that RHT/AGIL, previously shown to interact with CNBP, contains a highly flexible loop surrounded by more ordered helices. As one of the largest RNA-only 3-D studies, the work lays the foundation for future structural studies of lncRNA-protein complexes.	Jan 2020
B21-High Throughput SAXS I04-1-Macromolecular Crystallography (fixed wavelength)	Structure and mechanism of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate Stephen Mcmahon , Wenlong Zhu , Shirley Graham , Robert Rambo , Malcolm F. White , Tracey M. Gloster Nature Communications 11 DOI: 10.1038/s41467-019-14222-x Diamond Proposal Number(s): [19844, 21035] Open Access Show Abstract ▼ Abstract: The CRISPR system provides adaptive immunity against mobile genetic elements in prokaryotes. On binding invading RNA species, Type III CRISPR systems generate cyclic oligoadenylate (cOA) signalling molecules, potentiating a powerful immune response by activating downstream effector proteins, leading to viral clearance, cell dormancy or death. Here we describe the structure and mechanism of a cOA-activated CRISPR defence DNA endonuclease, CRISPR ancillary nuclease 1 (Can1). Can1 has a unique monomeric structure with two CRISPR associated Rossman fold (CARF) domains and two DNA nuclease-like domains. The crystal structure of the enzyme has been captured in the activated state, with a cyclic tetra-adenylate (cA4) molecule bound at the core of the protein. cA4 binding reorganises the structure to license a metal-dependent DNA nuclease activity specific for nicking of supercoiled DNA. DNA nicking by Can1 is predicted to slow down viral replication kinetics by leading to the collapse of DNA replication forks.	Jan 2020

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