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189 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
I03-Macromolecular Crystallography	Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera Piyada Supasa , Daming Zhou , Wanwisa Dejnirattisai , Chang Liu , Alexander J. Mentzer , Helen M. Ginn , Yuguang Zhao , Helen M. E. Duyvesteyn , Rungtiwa Nutalai , Aekkachai Tuekprakhon , Beibei Wang , Guido Paesen , Jose Slon-campos , César López-camacho , Bassam Hallis , Naomi Coombes , Kevin Bewley , Sue Charlton , Thomas S. Walter , Eleanor Barnes , Susanna J. Dunachie , Donal Skelly , Sheila F. Lumley , Natalie Baker , Imam Shaik , Holly Humphries , Kerry Godwin , Nick Gent , Alex Sienkiewicz , Christina Dold , Robert Levin , Tao Dong , Andrew J. Pollard , Julian C. Knight , Paul Klenerman , Derrick Crook , Teresa Lambe , Elizabeth Clutterbuck , Sagida Bibi , Amy Flaxman , Mustapha Bittaye , Sandra Belij-rammerstorfer , Sarah Gilbert , Dave R. Hall , Mark Williams , Neil G. Paterson , William James , Miles W. Carroll , Elizabeth E. Fry , Juthathip Mongkolsapaya , Jingshan Ren , David I. Stuart , Gavin R. Screaton Cell DOI: 10.1016/j.cell.2021.02.033 Diamond Proposal Number(s): [27009] Open Access Show Abstract ▼ Abstract: SARS-CoV-2 has caused over 2M deaths in little over a year. Vaccines are being deployed at scale, aiming to generate responses against the virus spike. The scale of the pandemic and error-prone virus replication is leading to the appearance of mutant viruses and potentially escape from antibody responses. Variant B.1.1.7, now dominant in the UK, with increased transmission, harbours 9 amino-acid changes in the spike, including N501Y in the ACE2 interacting-surface. We examine the ability of B.1.1.7 to evade antibody responses elicited by natural SARS-CoV-2 infection or vaccination. We map the impact of N501Y by structure/function analysis of a large panel of well-characterised monoclonal antibodies. B.1.1.7 is harder to neutralize than parental virus, compromising neutralization by some members of a major class of public antibodies through light chain contacts with residue 501. However, widespread escape from monoclonal antibodies or antibody responses generated by natural infection or vaccination was not observed.	Feb 2021
Krios IV-Titan Krios IV at Diamond	DNA origami signposts for identifying proteins on cell membranes by electron cryotomography Emma Silvester , Benjamin Vollmer , Vojtech Prazak , Daven Vasishtan , Emily A. Machala , Catheryne Whittle , Susan Black , Jonathan Bath , Andrew J. Turberfield , Kay Grunewald , Lindsay A. Baker Cell 184, 1110 - 1121.e16 DOI: 10.1016/j.cell.2021.01.033 Diamond Proposal Number(s): [20223] Open Access Show Abstract ▼ Abstract: Electron cryotomography (cryoET), an electron cryomicroscopy (cryoEM) modality, has changed our understanding of biological function by revealing the native molecular details of membranes, viruses, and cells. However, identification of individual molecules within tomograms from cryoET is challenging because of sample crowding and low signal-to-noise ratios. Here, we present a tagging strategy for cryoET that precisely identifies individual protein complexes in tomograms without relying on metal clusters. Our method makes use of DNA origami to produce “molecular signposts” that target molecules of interest, here via fluorescent fusion proteins, providing a platform generally applicable to biological surfaces. We demonstrate the specificity of signpost origami tags (SPOTs) in vitro as well as their suitability for cryoET of membrane vesicles, enveloped viruses, and the exterior of intact mammalian cells.	Feb 2021
I03-Macromolecular Crystallography	Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine induced sera 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 Cell DOI: 10.1016/j.cell.2021.02.037 Diamond Proposal Number(s): [27009] Open Access Show Abstract ▼ 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.	Feb 2021
B18-Core EXAFS B22-Multimode InfraRed imaging And Microspectroscopy I11-High Resolution Powder Diffraction	Catalytic decomposition of NO2 over a copper-decorated metal–organic framework by non-thermal plasma 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 Cell Reports Physical Science 3 DOI: 10.1016/j.xcrp.2021.100349 Open Access Show Abstract ▼ 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.	Feb 2021
I03-Macromolecular Crystallography Krios I-Titan Krios I at Diamond	The antigenic anatomy of SARS-CoV-2 receptor binding domain 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 Cell DOI: 10.1016/j.cell.2021.02.032 Diamond Proposal Number(s): [27009, 26983] Open Access Show Abstract ▼ 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.	Feb 2021
I03-Macromolecular Crystallography I04-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	A tamoxifen receptor within a voltage-gated sodium channel Altin Sula , David Hollingworth , Leo C. T. Ng , Megan Larmore , Paul G. Decaen , Bonnie A. Wallace Molecular Cell 350 DOI: 10.1016/j.molcel.2020.12.048 Diamond Proposal Number(s): [17201, 23853] Open Access Show Abstract ▼ Abstract: Voltage-gated sodium channels are targets for many analgesic and antiepileptic drugs whose therapeutic mechanisms and binding sites have been well characterized. We describe the identification of a previously unidentified receptor site within the NavMs voltage-gated sodium channel. Tamoxifen, an estrogen receptor modulator, and its primary and secondary metabolic products bind at the intracellular exit of the channel, which is a site that is distinct from other previously characterized sodium channel drug sites. These compounds inhibit NavMs and human sodium channels with similar potencies and prevent sodium conductance by delaying channel recovery from the inactivated state. This study therefore not only describes the structure and pharmacology of a site that could be leveraged for the development of new drugs for the treatment of sodium channelopathies but may also have important implications for off-target health effects of this widely used therapeutic drug.	Jan 2021
I11-High Resolution Powder Diffraction	Effect of anode slippage on cathode cutoff potential and degradation mechanisms in Ni-rich Li-ion batteries Wesley M. Dose , Chao Xu , Clare Grey , Michael F. L. De Volder Cell Reports Physical Science DOI: 10.1016/j.xcrp.2020.100253 Diamond Proposal Number(s): [25186] Open Access Show Abstract ▼ Abstract: Li-ion batteries based on Ni-rich layered cathodes are the state-of-the-art technology for electric vehicles; however, batteries using these advanced materials suffer from rapid performance fading. In this work, we report a critical turning point during the aging of graphite/LiNi0.8Mn0.1Co0.1O2 (NMC811) full cells, after which the degradation is significantly accelerated. This turning point was identified using differential voltage analysis (DVA) applied to standard two-electrode data, which shows that graphite becomes progressively less lithiated, as confirmed by operando long-duration X-ray diffraction, and therefore has a higher electrochemical potential at the end of charge. This increase leads to a proportional increase in the cathode potential, and an accelerated impedance increase is observed from this point. This mechanism is expected to be universal for the vast majority of Li-ion battery chemistries, particularly for Ni-rich cathodes, whose degradation is extremely sensitive to the upper cutoff voltage, and our work provides fundamental guidelines for developing effective countermeasures.	Nov 2020
I02-Macromolecular Crystallography I03-Macromolecular Crystallography	Hemagglutinin traits determine transmission of avian A/H10N7 influenza virus between mammals Sander Herfst , Jie Zhang , Mathilde Richard , Ryan Mcbride , Pascal Lexmond , Theo M. Bestebroer , Monique I. J. Spronken , Dennis De Meulder , Judith M. Van Den Brand , Miruna E. Rosu , Stephen R. Martin , Steven J. Gamblin , Xiaoli Xiong , Wenjie Peng , Rogier Bodewes , Erhard Van Der Vries , Albert D. M. E. Osterhaus , James C. Paulson , John J. Skehel , Ron A. M. Fouchier Cell Host & Microbe 28, 602 - 613.e7 DOI: 10.1016/j.chom.2020.08.011 Diamond Proposal Number(s): [9826, 13775] Show Abstract ▼ Abstract: In 2014, an outbreak of avian A/H10N7 influenza virus occurred among seals along North-European coastal waters, significantly impacting seal populations. Here, we examine the cross-species transmission and mammalian adaptation of this influenza A virus, revealing changes in the hemagglutinin surface protein that increase stability and receptor binding. The seal A/H10N7 virus was aerosol or respiratory droplet transmissible between ferrets. Compared with avian H10 hemagglutinin, seal H10 hemagglutinin showed stronger binding to the human-type sialic acid receptor, with preferential binding to α2,6-linked sialic acids on long extended branches. In X-ray structures, changes in the 220-loop of the receptor-binding pocket caused similar interactions with human receptor as seen for pandemic strains. Two substitutions made seal H10 hemagglutinin more stable than avian H10 hemagglutinin and similar to human hemagglutinin. Consequently, identification of avian-origin influenza viruses across mammals appears critical to detect influenza A viruses posing a major threat to humans and other mammals.	Oct 2020
I24-Microfocus Macromolecular Crystallography	Molecular basis of MKLP2-dependent Aurora B transport from chromatin to the anaphase central spindle Michela Serena , Ricardo Nunes Bastos , Paul R. Elliott , Francis A. Barr Journal Of Cell Biology 219 DOI: 10.1083/jcb.201910059 Diamond Proposal Number(s): [18069] Open Access Show Abstract ▼ Abstract: The Aurora B chromosomal passenger complex (CPC) is a conserved regulator of mitosis. Its functions require localization first to the chromosome arms and then centromeres in mitosis and subsequently the central spindle in anaphase. Here, we analyze the requirements for core CPC subunits, survivin and INCENP, and the mitotic kinesin-like protein 2 (MKLP2) in targeting to these distinct localizations. Centromere recruitment of the CPC requires interaction of survivin with histone H3 phosphorylated at threonine 3, and we provide a complete structure of this assembly. Furthermore, we show that the INCENP RRKKRR-motif is required for both centromeric localization of the CPC in metaphase and MKLP2-dependent transport in anaphase. MKLP2 and DNA bind competitively to this motif, and INCENP T59 phosphorylation acts as a switch preventing MKLP2 binding in metaphase. In anaphase, CPC binding promotes the microtubule-dependent ATPase activity of MKLP2. These results explain how centromere targeting of the CPC in mitosis is coupled to its movement to the central spindle in anaphase.	Jul 2020
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	CD4+ T cells recognize conserved influenza a epitopes through shared patterns of V-gene usage and complementary biochemical features Alexander Greenshields-watson , Meriem Attaf , Bruce J. Maclachlan , Thomas Whalley , Cristina Rius , Aaron Wall , Angharad Lloyd , Hywel Hughes , Kathryn E. Strange , Georgina H. Mason , Andrea J. Schauenburg , Sarah L. Hulin-curtis , James Geary , Yuan Chen , Sarah N. Lauder , Kathryn Smart , Dhanasekaran Vijaykrishna , Miguel L. Grau , Mikhail Shugay , Robert Andrews , Garry Dolton , Pierre J. Rizkallah , Awen M. Gallimore , Andrew K. Sewell , Andrew J. Godkin , David K. Cole Cell Reports 32 DOI: 10.1016/j.celrep.2020.107885 Diamond Proposal Number(s): [10462, 14843] Open Access Show Abstract ▼ Abstract: T cell recognition of peptides presented by human leukocyte antigens (HLAs) is mediated by the highly variable T cell receptor (TCR). Despite this built-in TCR variability, individuals can mount immune responses against viral epitopes by using identical or highly related TCRs expressed on CD8+ T cells. Characterization of these TCRs has extended our understanding of the molecular mechanisms that govern the recognition of peptide-HLA. However, few examples exist for CD4+ T cells. Here, we investigate CD4+ T cell responses to the internal proteins of the influenza A virus that correlate with protective immunity. We identify five internal epitopes that are commonly recognized by CD4+ T cells in five HLA-DR1+ subjects and show conservation across viral strains and zoonotic reservoirs. TCR repertoire analysis demonstrates several shared gene usage biases underpinned by complementary biochemical features evident in a structural comparison. These epitopes are attractive targets for vaccination and other T cell therapies.	Jul 2020

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