Search Results

You searched for all publications:

with publication states 'Published (Approved)'

Search Again...

These results only include publications that have been reviewed and processed by Diamond Light Source. To also view papers that have not yet been processed click here.

You can use the folder icon under Actions to collate papers as required. You can then click on View Folder in the left-hand navigation to review and/or download your folder.

Exact matches
Related results

25 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3 [Next/Last]

Instruments / Technical Area	Publication Details	Published
I03-Macromolecular Crystallography I04-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Clamping, bending, and twisting inter-domain motions in the misfold-recognizing portion of UDP-glucose:glycoprotein glucosyltransferase Carlos P. Modenutti , Juan I. Blanco Capurro , Roberta Ibba , Dominic S. Alonzi , Mauro N. Song , Snežana Vasiljević , Abhinav Kumar , Anu V. Chandran , Gabor Tax , Lucia Marti , Johan C. Hill , Andrea Lia , Mario Hensen , Thomas Waksman , Jonathan Rushton , Simone Rubichi , Angelo Santino , Marcelo A. Martí , Nicole Zitzmann , Pietro Roversi Structure DOI: 10.1016/j.str.2020.11.017 Diamond Proposal Number(s): [12346, 18069] Open Access Show Abstract ▼ Abstract: UDP-glucose:glycoprotein glucosyltransferase (UGGT) flags misfolded glycoproteins for ER retention. We report crystal structures of full-length Chaetomium thermophilum UGGT (CtUGGT), two CtUGGT double-cysteine mutants, and its TRXL2 domain truncation (CtUGGT-ΔTRXL2). CtUGGT molecular dynamics (MD) simulations capture extended conformations and reveal clamping, bending, and twisting inter-domain movements. We name “Parodi limit” the maximum distance on the same glycoprotein between a site of misfolding and an N-linked glycan that can be reglucosylated by monomeric UGGT in vitro, in response to recognition of misfold at that site. Based on the MD simulations, we estimate the Parodi limit as around 70–80 Å. Frequency distributions of distances between glycoprotein residues and their closest N-linked glycosylation sites in glycoprotein crystal structures suggests relevance of the Parodi limit to UGGT activity in vivo. Our data support a “one-size-fits-all adjustable spanner” UGGT substrate recognition model, with an essential role for the UGGT TRXL2 domain.	Dec 2020
I03-Macromolecular Crystallography	Partial catalytic Cys oxidation of human GAPDH Andrea Lia , Adam Dowle , Chris Taylor , Angelo Santino , Pietro Roversi Wellcome Open Research 5 DOI: 10.12688/wellcomeopenres.15893.2 Open Access Show Abstract ▼ Abstract: Background: n-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyses the reversible NAD+-dependent oxidative phosphorylation of n-glyceraldehyde-3-phosphate to 1,3-diphospho-n-glycerate in both glycolysis and gluconeogenesis. Methods: Four distinct crystal structures of human n-Glyceraldehyde-3-phosphate dehydrogenase (HsGAPDH) have been determined from protein purified from the supernatant of HEK293F human epithelial kidney cells. Results: X-ray crystallography and mass-spectrometry indicate that the catalytic cysteine of the protein (HsGAPDH Cys152) is partially oxidised to cysteine S-sulfonic acid. The average occupancy for the Cys152-S-sulfonic acid modification over the 20 crystallographically independent copies of HsGAPDH across three of the crystal forms obtained is 0.31±0.17. Conclusions: The modification induces no significant structural changes on the tetrameric enzyme, and only makes aspecific contacts to surface residues in the active site, in keeping with the hypothesis that the oxidising conditions of the secreted mammalian cell expression system result in HsGAPDH catalytic cysteine S-sulfonic acid modification and irreversible inactivation of the enzyme.	Jun 2020
I02-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength)	Targeting ER α-glucosidase I with a single-dose iminosugar treatment protects against lethal influenza and dengue virus infections Kelly Warfield , Dominic S. Alonzi , Johan C. Hill , Alessandro T. Caputo , Pietro Roversi , John I. Kiappes , Nicholas Sheets , Matthew Duchars , Raymond Dwek , Julia Biggins , Dale L. Barnard , Sujan Shresta , Anthony Treston , Nicole Zitzmann Journal Of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.0c00067 Diamond Proposal Number(s): [12346] Show Abstract ▼ Abstract: Influenza and dengue viruses present a growing global threat to public health. Both viruses depend on the host endoplasmic reticulum (ER) glycoprotein folding pathway. In 2014, Sadat et al. reported two siblings with a rare genetic defect in ER alpha-glucosidase I (ER Glu I) who showed resistance to viral infections, identifying ER Glu I as a key antiviral target. Here we show that a single dose of UV-4B (the hydrochloride salt form of N-(9′-methoxynonyl)-1- deoxynojirimycin; MON-DNJ) capable of inhibiting Glu I in vivo is sufficient to prevent death in mice infected with lethal viral doses, even when treatment is started as late as 48 hours post-infection. The first crystal structure of mammalian ER Glu I will constitute the basis for the development of potent and selective inhibitors. Targeting ER Glu I with UV-4B derived compounds may alter treatment paradigms for acute viral disease through development of a single-dose therapeutic regime.	Mar 2020
	Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016) Andriy Kryshtafovych , Reinhard Albrecht , Arnaud Basle , Pedro Bule , Alessandro T. Caputo , Ana Luisa Carvalho , Kinlin L. Chao , Ron Diskin , Krzysztof Fidelis , Carlos M. G. A. Fontes , Folmer Fredslund , Harry J. Gilbert , Celia W. Goulding , Marcus D. Hartmann , Christopher S. Hayes , Osnat Herzberg , Johan C. Hill , Andrzej Joachimiak , Gert-wieland Kohring , Roman I. Koning , Leila Lo Leggio , Marco Mangiagalli , Karolina Michalska , John Moult , Shabir Najmudin , Marco Nardini , Valentina Nardone , Didier Ndeh , Thanh-hong Nguyen , Guido Pintacuda , Sandra Postel , Mark J. Van Raaij , Pietro Roversi , Amir Shimon , Abhimanyu K. Singh , Eric J. Sundberg , Kaspars Tars , Nicole Zitzmann , Torsten Schwede Proteins: Structure, Function, And Bioinformatics 86, 27 - 50 DOI: 10.1002/prot.25392 Show Abstract ▼ Abstract: The functional and biological significance of the selected CASP12 targets are described by the authors of the structures. The crystallographers discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP12 experiment.	Mar 2018
I04-1-Macromolecular Crystallography (fixed wavelength) Krios I-Titan Krios I at Diamond	Interdomain conformational flexibility underpins the activity of UGGT, the eukaryotic glycoprotein secretion checkpoint Pietro Roversi , Lucia Marti , Alessandro T. Caputo , Dominic S. Alonzi , Johan C. Hill , Kyle C. Dent , Abhinav Kumar , Mikail D. Levasseur , Andrea Lia , Thomas Waksman , Souradeep Basu , Yentli Soto Albrecht , Kristin Qian , James Patrick Mcivor , Colette B. Lipp , Dritan Siliqi , Snezana Vasilijevic , Shabaz Mohammed , Petra Lukacik , Martin A. Walsh , Angelo Santino , Nicole Zitzmann Proceedings Of The National Academy Of Sciences Pnas DOI: 10.1073/pnas.1703682114 Show Abstract ▼ Abstract: Glycoproteins traversing the eukaryotic secretory pathway begin life in the endoplasmic reticulum (ER), where their folding is surveyed by the 170-kDa UDP-glucose:glycoprotein glucosyltransferase (UGGT). The enzyme acts as the single glycoprotein folding quality control checkpoint: it selectively reglucosylates misfolded glycoproteins, promotes their association with ER lectins and associated chaperones, and prevents premature secretion from the ER. UGGT has long resisted structural determination and sequence-based domain boundary prediction. Questions remain on how this single enzyme can flag misfolded glycoproteins of different sizes and shapes for ER retention and how it can span variable distances between the site of misfold and a glucose-accepting N-linked glycan on the same glycoprotein. Here, crystal structures of a full-length eukaryotic UGGT reveal four thioredoxin-like (TRXL) domains arranged in a long arc that terminates in two β-sandwiches tightly clasping the glucosyltransferase domain. The fold of the molecule is topologically complex, with the first β-sandwich and the fourth TRXL domain being encoded by nonconsecutive stretches of sequence. In addition to the crystal structures, a 15-Å cryo-EM reconstruction reveals interdomain flexibility of the TRXL domains. Double cysteine point mutants that engineer extra interdomain disulfide bridges rigidify the UGGT structure and exhibit impaired activity. The intrinsic flexibility of the TRXL domains of UGGT may therefore endow the enzyme with the promiscuity needed to recognize and reglucosylate its many different substrates and/or enable reglucosylation of N-linked glycans situated at variable distances from the site of misfold.	Jun 2017
I02-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Identification and characterization of a heterotrimeric archaeal DNA polymerase holoenzyme Jiangyu Yan , Thomas R. Beattie , Adriana L. Rojas , Kelly Schermerhorn , Tamzin Gristwood , Jonathan C. Trinidad , Sonja V. Albers , Pietro Roversi , Andrew F. Gardner , Nicola G. A. Abrescia , Stephen D. Bell Nature Communications 8 DOI: 10.1038/ncomms15075 Diamond Proposal Number(s): [9063, 10130] Open Access Show Abstract ▼ Abstract: Since their initial characterization over 30 years ago, it has been believed that the archaeal B-family DNA polymerases are single-subunit enzymes. This contrasts with the multi-subunit B-family replicative polymerases of eukaryotes. Here we reveal that the highly studied PolB1 from Sulfolobus solfataricus exists as a heterotrimeric complex in cell extracts. Two small subunits, PBP1 and PBP2, associate with distinct surfaces of the larger catalytic subunit and influence the enzymatic properties of the DNA polymerase. Thus, multi-subunit replicative DNA polymerase holoenzymes are present in all three domains of life. We reveal the architecture of the assembly by a combination of cross-linking coupled with mass spectrometry, X-ray crystallography and single-particle electron microscopy. The small subunits stabilize the holoenzyme assembly and the acidic tail of one small subunit mitigates the ability of the enzyme to perform strand-displacement synthesis, with important implications for lagging strand DNA synthesis.	May 2017
I02-Macromolecular Crystallography I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography	Structures of mammalian ER α-glucosidase II capture the binding modes of broad-spectrum iminosugar antivirals Alessandro T. Caputo , Dominic S. Alonzi , Lucia Marti , Ida-barbara Reca , John Kiappes , Weston B. Struwe , Alice Cross , Souradeep Basu , Ed Lowe , Benoit Darlot , Angelo Santino , Pietro Roversi , Nicole Zitzmann Proceedings Of The National Academy Of Sciences 113, E4630 - E4638 DOI: 10.1073/pnas.1604463113 Diamond Proposal Number(s): [9306] Show Abstract ▼ Abstract: The biosynthesis of enveloped viruses depends heavily on the host cell endoplasmic reticulum (ER) glycoprotein quality control (QC) machinery. This dependency exceeds the dependency of host glycoproteins, offering a window for the targeting of ERQC for the development of broad-spectrum antivirals. We determined small-angle X-ray scattering (SAXS) and crystal structures of the main ERQC enzyme, ER α-glucosidase II (α-GluII; from mouse), alone and in complex with key ligands of its catalytic cycle and antiviral iminosugars, including two that are in clinical trials for the treatment of dengue fever. The SAXS data capture the enzyme’s quaternary structure and suggest a conformational rearrangement is needed for the simultaneous binding of a monoglucosylated glycan to both subunits. The X-ray structures with key catalytic cycle intermediates highlight that an insertion between the +1 and +2 subsites contributes to the enzyme’s activity and substrate specificity, and reveal that the presence of d-mannose at the +1 subsite renders the acid catalyst less efficient during the cleavage of the monoglucosylated substrate. The complexes with iminosugar antivirals suggest that inhibitors targeting a conserved ring of aromatic residues between the α-GluII +1 and +2 subsites would have increased potency and selectivity, thus providing a template for further rational drug design.	Aug 2016
I04-1-Macromolecular Crystallography (fixed wavelength) I24-Microfocus Macromolecular Crystallography	Super-complexes of adhesion GPCRs and neural guidance receptors Verity A. Jackson , Shahid Mehmood , Matthieu Chavent , Pietro Roversi , Maria Carrasquero , Daniel Del Toro , Goenuel Seyit-bremer , Fanomezana M. Ranaivoson , Davide Comoletti , Mark S. P. Sansom , Carol V. Robinson , Rüdiger Klein , Elena Seiradake Nature Communications 7 DOI: 10.1038/ncomms11184 Diamond Proposal Number(s): [9306, 8423, 1747] Open Access Show Abstract ▼ Abstract: Latrophilin adhesion-GPCRs (Lphn1–3 or ADGRL1–3) and Unc5 cell guidance receptors (Unc5A–D) interact with FLRT proteins (FLRT1–3), thereby promoting cell adhesion and repulsion, respectively. How the three proteins interact and function simultaneously is poorly understood. We show that Unc5D interacts with FLRT2 in cis, controlling cell adhesion in response to externally presented Lphn3. The ectodomains of the three proteins bind cooperatively. Crystal structures of the ternary complex formed by the extracellular domains reveal that Lphn3 dimerizes when bound to FLRT2:Unc5, resulting in a stoichiometry of 1:1:2 (FLRT2:Unc5D:Lphn3). This 1:1:2 complex further dimerizes to form a larger ‘super-complex’ (2:2:4), using a previously undescribed binding motif in the Unc5D TSP1 domain. Molecular dynamics simulations, point-directed mutagenesis and mass spectrometry demonstrate the stability and molecular properties of these complexes. Our data exemplify how receptors increase their functional repertoire by forming different context-dependent higher-order complexes.	Apr 2016
I04-Macromolecular Crystallography	Structural Basis of Latrophilin-FLRT Interaction Verity Jackson , Daniel Del toro , Maria Carrasquero , Pietro Roversi , Karl Harlos , Rüdiger Klein , Elena Seiradake Structure DOI: 10.1016/j.str.2015.01.013 PMID: 25728924 Diamond Proposal Number(s): [10627] Open Access Show Abstract ▼ Abstract: Jackson et al. describe a crystal structure of mLPHN3 lectin and olfactomedin-like (Olf) domains, revealing the Olf b-propeller fold and calcium-binding site. Assays using HeLa cells and cortical neurons reveal a bi-functional role for Olf and its ligand FLRT, leading to HeLa cell adhesion and neuron repulsion.	Apr 2015
I02-Macromolecular Crystallography I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography	Expression levels of MHC class I molecules are inversely correlated with promiscuity of peptide binding Paul Chappell , El Kahina Meziane , Michael Harrison , Łukasz Magiera , Clemens Hermann , Laura Mears , Antoni G Wrobel , Charlotte Durant , Lise Lotte Nielsen , Søren Buus , Nicola Ternette , William Mwangi , Colin Butter , Venugopal Nair , Trudy Ahyee , Richard Duggleby , Alejandro Madrigal , Pietro Roversi , Susan Lea , Jim Kaufman Elife 4 DOI: 10.7554/eLife.05345 PMID: 25860507 Diamond Proposal Number(s): [9306] Open Access Show Abstract ▼ Abstract: Highly polymorphic major histocompatibility complex (MHC) molecules are at the heart of adaptive immune responses, playing crucial roles in many kinds of disease and in vaccination. We report that breadth of peptide presentation and level of cell surface expression of class I molecules are inversely correlated in both chickens and humans. This relationship correlates with protective responses against infectious pathogens including Marek's disease virus leading to lethal tumours in chickens and human immunodeficiency virus infection progressing to AIDS in humans. We propose that differences in peptide binding repertoire define two groups of MHC class I molecules strategically evolved as generalists and specialists for different modes of pathogen resistance. We suggest that differences in cell surface expression level ensure the development of optimal peripheral T cell responses. The inverse relationship of peptide repertoire and expression is evidently a fundamental property of MHC molecules, with ramifications extending beyond immunology and medicine to evolutionary biology and conservation. - See more at: http://elifesciences.org/content/4/e05345#sthash.zKFHdAeD.dpuf	Apr 2015

Publications Database

Search Results

You searched for all publications:

Search Again...

Subject Areas (check all that apply) select all

Instruments used to collect data (check all that apply) select all

Collaborations involved (check all that apply) select all

Diamond Offline Facilities used

Relevant Technical Areas (check all that apply) select all

Menu for Anonymous User