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

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

Instruments / Technical Area	Publication Details	Published
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	HLA A24:02–restricted T cell receptors cross-recognize bacterial and preproinsulin peptides in type 1 diabetes Garry Dolton , Anna Bulek , Aaron Wall , Hannah Thomas , Jade R. Hopkins , Cristina Rius , Sarah A. E. Galloway , Thomas Whalley , Li Rong Tan , Théo Morin , Nader Omidvar , Anna Fuller , Katie Topley , Md Samiul Hasan , Shikha Jain , Nirupa D’souza , Thomas Hodges-Hoyland , Owen B. Spiller , Deborah Kronenberg-Versteeg , Barbara Szomolay , Hugo A. Van Den Berg , Lucy C. Jones , Mark Peakman , David K. Cole , Pierre J. Rizkallah , Andrew K. Sewell Journal Of Clinical Investigation 134* DOI: 10.1172/JCI164535 Diamond Proposal Number(s): [10462, 18812] Open Access Show Abstract ▼ Abstract: CD8+ T cells destroy insulin-producing pancreatic β cells in type 1 diabetes through HLA class I–restricted presentation of self-antigens. Combinatorial peptide library screening was used to produce a preferred peptide recognition landscape for a patient-derived T cell receptor (TCR) that recognized the preproinsulin-derived (PPI-derived) peptide sequence LWMRLLPLL in the context of disease risk allele HLA A24:02. Data were used to generate a strong superagonist peptide, enabling production of an autoimmune HLA A24:02–peptide–TCR structure by crystal seeding. TCR binding to the PPI epitope was strongly focused on peptide residues Arg4 and Leu5, with more flexibility at other positions, allowing the TCR to strongly engage many peptides derived from pathogenic bacteria. We confirmed an epitope from Klebsiella that was recognized by PPI-reactive T cells from 3 of 3 HLA A24:02+ patients. Remarkably, the same epitope selected T cells from 7 of 8 HLA A24+ healthy donors that cross-reacted with PPI, leading to recognition and killing of HLA A*24:02+ cells expressing PPI. These data provide a mechanism by which molecular mimicry between pathogen and self-antigens could have resulted in the breaking of self-tolerance to initiate disease.	Sep 2024
I03-Macromolecular Crystallography	A targeted single mutation in influenza A virus universal epitope transforms immunogenicity and protective immunity via CD4+ T cell activation Sarah Hulin-Curtis , James K. Geary , Bruce J. Maclachlan , Danny M. Altmann , Laury Baillon , David K. Cole , Alexander Greenshields-Watson , Sophie J. Hesketh , Ian R. Humphreys , Ian M. Jones , Sarah N. Lauder , Georgina H. Mason , Kathryn Smart , D. Oliver Scourfield , Jake Scott , Ksenia Sukhova , Richard J. Stanton , Aaron Wall , Pierre J. Rizkallah , Wendy S. Barclay , Awen Gallimore , Andrew Godkin Cell Reports 43 DOI: 10.1016/j.celrep.2024.114259 Diamond Proposal Number(s): [10462] Open Access Show Abstract ▼ Abstract: CD4+ T cells are central to adaptive immunity. Their role in cross-protection in viral infections such as influenza and severe acute respiratory syndrome (SARS) is well documented; however, molecular rules governing T cell receptor (TCR) engagement of peptide-human leukocyte antigen (pHLA) class II are less understood. Here, we exploit an aspect of HLA class II presentation, the peptide-flanking residues (PFRs), to “tune” CD4+ T cell responses within an in vivo model system of influenza. Using a recombinant virus containing targeted substitutions at immunodominant HLA-DR1 epitopes, we demonstrate limited weight loss and improved clinical scores after heterosubtypic re-challenge. We observe enhanced protection linked to lung-derived influenza-specific CD4+ and CD8+ T cells prior to re-infection. Structural analysis of the ternary TCR:pHLA complex identifies that flanking amino acids influence side chains in the core 9-mer peptide, increasing TCR affinity. Augmentation of CD4+ T cell immunity is achievable with a single mutation, representing a strategy to enhance adaptive immunity that is decoupled from vaccine modality.	Jun 2024
I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography	Broad sialic acid usage amongst species D human adenovirus Rosie M. Mundy , Alexander T. Baker , Emily A. Bates , Tabitha G. Cunliffe , Alicia Teijeira-Crespo , Elise Moses , Pierre J. Rizkallah , Alan L. Parker Npj Viruses 1 DOI: 10.1038/s44298-023-00001-5 Diamond Proposal Number(s): [18812, 20147, 29990] Open Access Show Abstract ▼ Abstract: Human adenoviruses (HAdV) are widespread pathogens causing usually mild infections. The Species D (HAdV-D) cause gastrointestinal tract infections and epidemic keratoconjunctivitis (EKC). Despite being significant pathogens, knowledge around HAdV-D mechanism of cell infection is lacking. Sialic acid (SA) usage has been proposed as a cell infection mechanism for EKC causing HAdV-D. Here we highlight an important role for SA engagement by many HAdV-D. We provide apo state crystal structures of 7 previously undetermined HAdV-D fiber-knob proteins, and structures of HAdV-D25, D29, D30 and D53 fiber-knob proteins in complex with SA. Biologically, we demonstrate that removal of cell surface SA reduced infectivity of HAdV-C5 vectors pseudotyped with HAdV-D fiber-knob proteins, whilst engagement of the classical HAdV receptor CAR was variable. Our data indicates variable usage of SA and CAR across HAdV-D. Better defining these interactions will enable improved development of antivirals and engineering of the viruses into refined therapeutic vectors.	Sep 2023
I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography	Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4+ T cell immunity Yuan Chen , Georgina H. Mason , D. Oliver Scourfield , Alexander Greenshields-Watson , Tracey A. Haigh , Andrew K. Sewell , Heather M. Long , Awen M. Gallimore , Pierre Rizkallah , Bruce J. Maclachlan , Andrew Godkin Cell Reports 42 DOI: 10.1016/j.celrep.2023.112827 Diamond Proposal Number(s): [20147, 29502, 29990] Open Access Show Abstract ▼ Abstract: CD4+ T cells recognize a broad range of peptide epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which contribute to immune memory and limit COVID-19 disease. We demonstrate that the immunogenicity of SARS-CoV-2 peptides, in the context of the model allotype HLA-DR1, does not correlate with their binding affinity to the HLA heterodimer. Analyzing six epitopes, some with very low binding affinity, we solve X-ray crystallographic structures of each bound to HLA-DR1. Further structural definitions reveal the precise molecular impact of viral variant mutations on epitope presentation. Omicron escaped ancestral SARS-CoV-2 immunity to two epitopes through two distinct mechanisms: (1) mutations to TCR-facing epitope positions and (2) a mechanism whereby a single amino acid substitution caused a register shift within the HLA binding groove, completely altering the peptide-HLA structure. This HLA-II-specific paradigm of immune escape highlights how CD4+ T cell memory is finely poised at the level of peptide-HLA-II presentation.	Aug 2023
I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography	Targeting of multiple tumor-associated antigens by individual T cell receptors during successful cancer immunotherapy Garry Dolton , Cristina Rius , Aaron Wall , Barbara Szomolay , Valentina Bianchi , Sarah A. E. Galloway , Md Samiul Hasan , Théo Morin , Marine E. Caillaud , Hannah L. Thomas , Sarah Theaker , Li Rong Tan , Anna Fuller , Katie Topley , Mateusz Legut , Meriem Attaf , Jade R. Hopkins , Enas Behiry , Joanna Zabkiewicz , Caroline Alvares , Angharad Lloyd , Amber Rogers , Peter Henley , Christopher Fegan , Oliver Ottmann , Stephen Man , Michael D. Crowther , Marco Donia , Inge Marie Svane , David K. Cole , Paul E. Brown , Pierre Rizkallah , Andrew K. Sewell Cell 33 DOI: 10.1016/j.cell.2023.06.020 Open Access Show Abstract ▼ Abstract: The T cells of the immune system can target tumors and clear solid cancers following tumor-infiltrating lymphocyte (TIL) therapy. We used combinatorial peptide libraries and a proteomic database to reveal the antigen specificities of persistent cancer-specific T cell receptors (TCRs) following successful TIL therapy for stage IV malignant melanoma. Remarkably, individual TCRs could target multiple different tumor types via the HLA A∗02:01-restricted epitopes EAAGIGILTV, LLLGIGILVL, and NLSALGIFST from Melan A, BST2, and IMP2, respectively. Atomic structures of a TCR bound to all three antigens revealed the importance of the shared x-x-x-A/G-I/L-G-I-x-x-x recognition motif. Multi-epitope targeting allows individual T cells to attack cancer in several ways simultaneously. Such “multipronged” T cells exhibited superior recognition of cancer cells compared with conventional T cell recognition of individual epitopes, making them attractive candidates for the development of future immunotherapies.	Jul 2023
I03-Macromolecular Crystallography	The crystal structure of Bacillus thuringiensis Tpp80Aa1 and its interaction with galactose-containing glycolipids Hannah L. Best , Lainey J. Williamson , Magdalena Lipka-Lloyd , Helen Waller-Evans , Emyr Lloyd-Evans , Pierre J. Rizkallah , Colin Berry Toxins 14 DOI: 10.3390/toxins14120863 Diamond Proposal Number(s): [20147] Open Access Show Abstract ▼ Abstract: Tpp80Aa1 from Bacillus thuringiensis is a Toxin_10 family protein (Tpp) with reported action against Culex mosquitoes. Here, we demonstrate an expanded target range, showing Tpp80Aa1 is also active against the larvae of Anopheles gambiae and Aedes aegypti mosquitoes. We report the first crystal structure of Tpp80Aa1 at a resolution of 1.8 Å, which shows Tpp80Aa1 consists of two domains: an N-terminal β-trefoil domain resembling a ricin B lectin and a C-terminal putative pore-forming domain sharing structural similarity with the aerolysin family. Similar to other Tpp family members, we observe Tpp80Aa1 binds to the mosquito midgut, specifically the posterior midgut and the gastric caecum. We also identify that Tpp80Aa1 can interact with galactose-containing glycolipids and galactose, and this interaction is critical for exerting full insecticidal action against mosquito target cell lines.	Dec 2022
I04-1-Macromolecular Crystallography (fixed wavelength)	Emergence of immune escape at dominant SARS-CoV-2 killer T-cell epitope Garry Dolton , Cristina Rius , Md Samiul Hasan , Aaron Wall , Barbara Szomolay , Enas Behiry , Thomas Whalley , Joel Southgate , Anna Fuller , Théo Morin , Katie Topley , Li Rong Tan , Philip J. R. Goulder , Owen B. Spiller , Pierre J. Rizkallah , Lucy C. Jones , Thomas R. Connor , Andrew K. Sewell Cell DOI: 10.1016/j.cell.2022.07.002 Diamond Proposal Number(s): [29502] Open Access Show Abstract ▼ Abstract: We studied the prevalent cytotoxic CD8 T-cell response mounted against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike glycoprotein269-277 epitope (sequence YLQPRTFLL) via the most frequent Human Leukocyte Antigen (HLA) class I worldwide, HLA A∗02. The Spike P272L mutation that has arisen in at least 112 different SARS-CoV-2 lineages to date, including in lineages classified as ‘variants of concern’, was not recognised by the large CD8 T-cell response seen across cohorts of HLA A∗02+ convalescent patients and individuals vaccinated against SARS-CoV-2, despite these responses comprising of over 175 different individual T-cell receptors. Viral escape at prevalent T-cell epitopes restricted by high frequency HLAs may be particularly problematic when vaccine immunity is focussed on a single protein such as SARS-CoV-2 Spike providing a strong argument for inclusion of multiple viral proteins in next generation vaccines and highlighting the need for monitoring T-cell escape in new SARS-CoV-2 variants.	Jul 2022
I04-1-Macromolecular Crystallography (fixed wavelength)	Development of a low seroprevalence, αvβ6 integrin selective virotherapy based on human adenovirus type 10 Emily A. Bates , James A. Davies , Jana Váňová , Davor Nestić , Valerie S. Meniel , Sarah Koushyar , Tabitha G. Cunliffe , Rosie M. Mundy , Elise Moses , Hanni K. Uusi-Kerttula , Alexander T. Baker , David K. Cole , Dragomira Majhen , Pierre J. Rizkallah , Toby Phesse , John D. Chester , Alan L. Parker Molecular Therapy - Oncolytics DOI: 10.1016/j.omto.2022.03.007 Diamond Proposal Number(s): [18812] Open Access Show Abstract ▼ Abstract: Oncolytic virotherapies (OV) hold immense clinical potential. OV based on human adenoviruses (HAdV) derived from HAdV with naturally low rates of pre-existing immunity will be beneficial for future clinical translation. We generated a low seroprevalence HAdV-D10 serotype vector incorporating an αvβ6 integrin selective peptide, A20, to target αvβ6 positive tumour cell types. HAdV-D10 has limited natural tropism. Structural and biological studies of HAdV-D10 knob protein highlighted low affinity engagement with native adenoviral receptors CAR and sialic acid. HAdV-D10 fails to engage blood coagulation Factor X, potentially eliminating “off-target” hepatic sequestration in vivo. We engineered A20 peptide that selectively binds αvβ6 integrin into the DG loop of HAdV-D10 fiber knob. Assays in αvβ6+ cancer cell lines, demonstrated significantly increased transduction mediated by αvβ6 targeted variants compared to controls, confirmed microscopically. HAdV-D10.A20 resisted neutralization by neutralizing HAdV-C5 sera. Systemic delivery of HAdV-D10.A20 resulted in significantly increased GFP expression in BT20 tumours. Replication competent HAdV-D10.A20 demonstrated αvβ6 integrin selective cell killing in vitro and in vivo. HAdV-D10 possesses characteristics of a promising virotherapy, combining low seroprevalence, weak receptor interactions and reduced off-target uptake. Incorporation of an αvβ6 integrin selective peptide resulted in HAdV-D10.A20, with significant potential for clinical translation.	Mar 2022
I03-Macromolecular Crystallography	Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanism Nehad Noby , Husam Sabah Auhim , Samuel Winter , Harley L. Worthy , Amira M. Embaby , Hesham Saeed , Ahmed Hussein , Christopher R. Pudney , Pierre J. Rizkallah , Stephen A. Wells , D. Dafydd Jones Open Biology 11 DOI: 10.1098/rsob.210182 Diamond Proposal Number(s): [18812] Open Access Show Abstract ▼ Abstract: Here we determined the structure of a cold active family IV esterase (EstN7) cloned from Bacillus cohnii strain N1. EstN7 is a dimer with a classical α/β hydrolase fold. It has an acidic surface that is thought to play a role in cold-adaption by retaining solvation under changed water solvent entropy at lower temperatures. The conformation of the functionally important cap region is significantly different to EstN7's closest relatives, forming a bridge-like structure with reduced helical content providing greater access to the active site through more than one substrate access tunnel. However, dynamics do not appear to play a major role in cold adaption. Molecular dynamics at different temperatures, rigidity analysis, normal mode analysis and geometric simulations of motion confirm the flexibility of the cap region but suggest that the rest of the protein is largely rigid. Rigidity analysis indicates the distribution of hydrophobic tethers is appropriate to colder conditions, where the hydrophobic effect is weaker than in mesophilic conditions due to reduced water entropy. Thus, it is likely that increased substrate accessibility and tolerance to changes in water entropy are important for of EstN7's cold adaptation rather than changes in dynamics.	Dec 2021
I03-Macromolecular Crystallography	ChAdOx1 interacts with CAR and PF4 with implications for thrombosis with thrombocytopenia syndrome Alexander T. Baker , Ryan J. Boyd , Daipayan Sarkar , Alicia Teijeira-Crespo , Chun Kit Chan , Emily Bates , Kasim Waraich , John Vant , Eric Wilson , Chloe D. Truong , Magdalena Lipka-Lloyd , Petra Fromme , Josh Vermaas , Dewight Williams , Leeann Machiesky , Meike Heurich , Bolni M. Nagalo , Lynda Coughlan , Scott Umlauf , Po-Lin Chiu , Pierre J. Rizkallah , Taylor S. Cohen , Alan L. Parker , Abhishek Singharoy , Mitesh J. Borad Science Advances 7 DOI: 10.1126/sciadv.abl8213 Diamond Proposal Number(s): [20147] Open Access Show Abstract ▼ Abstract: Vaccines derived from chimpanzee adenovirus Y25 (ChAdOx1), human adenovirus type 26 (HAdV-D26), and human adenovirus type 5 (HAdV-C5) are critical in combatting the severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic. As part of the largest vaccination campaign in history, ultrarare side effects not seen in phase 3 trials, including thrombosis with thrombocytopenia syndrome (TTS), a rare condition resembling heparin-induced thrombocytopenia (HIT), have been observed. This study demonstrates that all three adenoviruses deployed as vaccination vectors versus SARS-CoV-2 bind to platelet factor 4 (PF4), a protein implicated in the pathogenesis of HIT. We have determined the structure of the ChAdOx1 viral vector and used it in state-of-the-art computational simulations to demonstrate an electrostatic interaction mechanism with PF4, which was confirmed experimentally by surface plasmon resonance. These data confirm that PF4 is capable of forming stable complexes with clinically relevant adenoviruses, an important step in unraveling the mechanisms underlying TTS.	Dec 2021

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