I04-1-Macromolecular Crystallography (fixed wavelength)
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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
Diamond Proposal Number(s):
[18812]
Open Access
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.
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Mar 2022
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I03-Macromolecular Crystallography
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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
Diamond Proposal Number(s):
[18812]
Open Access
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.
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Dec 2021
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I03-Macromolecular Crystallography
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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
Diamond Proposal Number(s):
[20147]
Open Access
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.
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Dec 2021
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
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Stephen
Man
,
James E.
Redman
,
Deborah L.
Cross
,
David K.
Cole
,
Ilona
Can
,
Bethan
Davies
,
Shaikh Shimaz
Hashimdeen
,
Reiss
Reid
,
Sian
Llewellyn-Lacey
,
Kelly L.
Miners
,
Kristin
Ladell
,
Anya
Lissina
,
Paul E.
Brown
,
Linda
Wooldridge
,
David A.
Price
,
Pierre J.
Rizkallah
Diamond Proposal Number(s):
[10462, 14843]
Abstract: The human CD8+ T cell clone 6C5 has previously been shown to recognize the tert-butyl-modified Bax161–170 peptide LLSY(3-tBu)FGTPT presented by HLA-A*02:01. This nonnatural epitope was likely created as a by-product of fluorenylmethoxycarbonyl protecting group peptide synthesis and bound poorly to HLA-A*02:01. In this study, we used a systematic approach to identify and characterize natural ligands for the 6C5 TCR. Functional analyses revealed that 6C5 T cells only recognized the LLSYFGTPT peptide when tBu was added to the tyrosine residue and did not recognize the LLSYFGTPT peptide modified with larger (di-tBu) or smaller chemical groups (Me). Combinatorial peptide library screening further showed that 6C5 T cells recognized a series of self-derived peptides with dissimilar amino acid sequences to LLSY(3-tBu)FGTPT. Structural studies of LLSY(3-tBu)FGTPT and two other activating nonamers (IIGWMWIPV and LLGWVFAQV) in complex with HLA-A*02:01 demonstrated similar overall peptide conformations and highlighted the importance of the position (P) 4 residue for T cell recognition, particularly the capacity of the bulky amino acid tryptophan to substitute for the tBu-modified tyrosine residue in conjunction with other changes at P5 and P6. Collectively, these results indicated that chemical modifications directly altered the immunogenicity of a synthetic peptide via molecular mimicry, leading to the inadvertent activation of a T cell clone with unexpected and potentially autoreactive specificities
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Jul 2021
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Diamond Proposal Number(s):
[18812]
Open Access
Abstract: The Hbl toxin is a three-component haemolytic complex produced by Bacillus cereus sensu lato strains and implicated as a cause of diarrhoea in B. cereus food poisoning. While the structure of the HblB component of this toxin is known, the structures of the other components are unresolved. Here, we describe the expression of the recombinant HblL1 component and the elucidation of its structure to 1.36 Å. Like HblB, it is a member of the alpha-helical pore-forming toxin family. In comparison to other members of this group, it has an extended hydrophobic beta tongue region that may be involved in pore formation. Molecular docking was used to predict possible interactions between HblL1 and HblB, and suggests a head to tail dimer might form, burying the HblL1 beta tongue region.
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Mar 2021
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Husam Sabah
Auhim
,
Bella L.
Grigorenko
,
Tessa K.
Harris
,
Ozan E.
Aksakal
,
Igor V.
Polyakov
,
Colin
Berry
,
Gabriel Dos Passos
Gomes
,
Igor V.
Alabugin
,
Pierre J.
Rizkallah
,
Alexander V.
Nemukhin
,
D. Dafydd
Jones
Diamond Proposal Number(s):
[18812]
Open Access
Abstract: Fluorescent proteins (FPs) have revolutionised the life sciences, but the mechanism of chromophore maturation is still not fully understood. Here we show that incorporation of a photo-responsive non-canonical amino acid within the chromophore stalls maturation of Venus, a yellow FP, at an intermediate stage; a crystal structure indicates the presence of O2 located above a dehydrated enolate form of the imidazolone ring, close to the strictly conserved Gly67 that occupies a twisted conformation. His148 adopts an “open” conformation so forming a channel that allows O2 access to the immature chromophore. Absorbance spectroscopy supported by QM/MM simulations suggests that the first oxidation step involves formation of a hydroperoxyl intermediate in conjunction with dehydrogenation of the methylene bridge. A fully conjugated mature chromophore is formed through release of H2O2, both in vitro and in vivo. The possibility of interrupting and photochemically restarting chromophore maturation and the mechanistic insights open up new approaches for engineering optically controlled fluorescent proteins.
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Mar 2021
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[18812]
Open Access
Abstract: The human adenovirus (HAdV) phylogenetic tree is diverse, divided across seven species and comprising over 100 individual types. Species D HAdV are rarely isolated with low rates of pre-existing immunity, making them appealing for therapeutic applications. Several species D vectors have been developed as vaccines against infectious diseases where they induce robust immunity in pre-clinical models and early phase clinical trials. However, many aspects of the basic virology of species D HAdV, including their basic receptor usage and means of cell entry, remain understudied.
Here, we investigated HAdV-D49, which previously has been studied for vaccine and vascular gene transfer applications. We generated a pseudotyped HAdV-C5 presenting the HAdV-D49 fiber knob protein (HAdV-C5/D49K). This pseudotyped vector was efficient at infecting cells devoid of all known HAdV receptors, indicating HAdV-D49 uses an unidentified cellular receptor. Conversely, a pseudotyped vector presenting the fiber knob protein of the closely related HAdV-D30 (HAdV-C5/D30K), differing in four amino acids to HAdV-D49, failed to demonstrate the same tropism. These four amino acid changes resulted in a change in isoelectric point of the knob protein, with HAdV-D49K possessing a basic apical region compared to a more acidic region in HAdV-D30K. Structurally and biologically we demonstrate that HAdV-D49 knob protein is unable to engage CD46, while potential interaction with CAR is extremely limited by extension of the DG loop. HAdV-C5/49K efficiently transduced cancer cell lines of pancreatic, breast, lung, oesophageal and ovarian origin, indicating it may have potential for oncolytic virotherapy applications, especially for difficult to transduce tumor types.
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Dec 2020
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I02-Macromolecular Crystallography
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Jacob R.
Pope
,
Rachel L.
Johnson
,
W. David
Jamieson
,
Harley L.
Worthy
,
Senthilkumar
Kailasam
,
Rochelle D.
Ahmed
,
Ismail
Taban
,
Husam Sabah
Auhim
,
Daniel W.
Watkins
,
Pierre J.
Rizkallah
,
Oliver K.
Castell
,
Dafydd
Jones
Diamond Proposal Number(s):
[10462]
Open Access
Abstract: Fluorescent proteins (FPs) are commonly used in pairs to monitor dynamic biomolecular events through changes in proximity via distance dependent processes such as Förster resonance energy transfer (FRET). The impact of FP association is assessed by predicting dimerization sites in silico and stabilizing the dimers by bio‐orthogonal covalent linkages. In each tested case dimerization changes inherent fluorescence, including FRET. GFP homodimers demonstrate synergistic behavior with the dimer being brighter than the sum of the monomers. The homodimer structure reveals the chromophores are close with favorable transition dipole alignments and a highly solvated interface. Heterodimerization (GFP with Venus) results in a complex with ≈87% FRET efficiency, significantly below the 99.7% efficiency predicted. A similar efficiency is observed when the wild‐type FPs are fused to a naturally occurring protein–protein interface system. GFP complexation with mCherry results in loss of mCherry fluorescence. Thus, simple assumptions used when monitoring interactions between proteins via FP FRET may not always hold true, especially under conditions whereby the protein–protein interactions promote FP interaction.
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Nov 2020
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I03-Macromolecular Crystallography
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Open Access
Abstract: The CD8 T cell response to the HLA-A2-restricted epitope LLWNGPMAV (LLW) of the non-structural protein 4b of Yellow Fever Virus (YFV) is remarkably immunodominant, highly prevalent and powerful in YFV-vaccinated humans. Here we used a combinatorial peptide library screening in the context of an A2/LLW-specific CD8 T cell clone to identify a superagonist that features a methionine to isoleucine substitution at position 7. Based on in silico modeling, the functional enhancement of this LLW-7I mutation was associated with alterations in the structural dynamics of the peptide in the major histocompatibility complex (pMHC) binding with the T cell receptor (TCR). While the TCR off-rate of LLW-7I pMHC is comparable to the wild type peptide, the rigidity of the 7I peptide seems to confer less entropy loss upon TCR binding. This LLW-7I superagonist is an example of improved functionality in human CD8 T cells associated with optimized ligand rigidity for TCR binding and not with changes in TCR:pMHC off-rate kinetics.
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Sep 2020
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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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
Diamond Proposal Number(s):
[10462, 14843]
Open Access
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.
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Jul 2020
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