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

9 items found (0 items not approved), displaying all items.1

Instruments / Technical Area	Publication Details	Published
I03-Macromolecular Crystallography	Target highlights in CASP14 : Analysis of models by structure providers Leila T. Alexander , Rosalba Lepore , Andriy Kryshtafovych , Athanasios Adamopoulos , Markus Alahuhta , Ann M. Arvin , Yannick J. Bomble , Bettina Böttcher , Cécile Breyton , Valerio Chiarini , Naga Babu Chinnam , Wah Chiu , Krzysztof Fidelis , Rhys Grinter , Gagan D. Gupta , Marcus D. Hartmann , Christopher S. Hayes , Tatjana Heidebrecht , Andrea Ilari , Andrzej Joachimiak , Youngchang Kim , Romain Linares , Andrew L. Lovering , Vladimir V. Lunin , Andrei N. Lupas , Cihan Makbul , Karolina Michalska , John Moult , Prasun K. Mukherjee , William Nutt , Stefan L. Oliver , Anastassis Perrakis , Lucy Stols , John A. Tainer , Maya Topf , Susan E. Tsutakawa , Mauricio Valdivia‐delgado , Torsten Schwede Proteins: Structure, Function, And Bioinformatics 89, 1647 - 1672 DOI: 10.1002/prot.26247 Open Access Show Abstract ▼ Abstract: The biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins.	Dec 2021
I02-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I24-Microfocus Macromolecular Crystallography	The structure of a conserved domain of TamB reveals a hydrophobic β taco fold Inokentijs Josts , Christopher James Stubenrauch , Grishma Vadlamani , Khedidja Mosbahi , Daniel Walker , Trevor Lithgow , Rhys Grinter Structure DOI: 10.1016/j.str.2017.10.002 Diamond Proposal Number(s): [6638, 8659] Open Access Show Abstract ▼ Abstract: The translocation and assembly module (TAM) plays a role in the transport and insertion of proteins into the bacterial outer membrane. TamB, a component of this system spans the periplasmic space to engage with its partner protein TamA. Despite efforts to characterize the TAM, the structure and mechanism of action of TamB remained enigmatic. Here we present the crystal structure of TamB amino acids 963–1,138. This region represents half of the conserved DUF490 domain, the defining feature of TamB. TamB963-1138 consists of a concave, taco-shaped β sheet with a hydrophobic interior. This β taco structure is of dimensions capable of accommodating and shielding the hydrophobic side of an amphipathic β strand, potentially allowing TamB to chaperone nascent membrane proteins from the aqueous environment. In addition, sequence analysis suggests that the structure of TamB963-1138 is shared by a large portion of TamB. This architecture could allow TamB to act as a conduit for membrane proteins.	Nov 2017
I02-Macromolecular Crystallography I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Structure of the bacterial plant-ferredoxin receptor FusA Rhys Grinter , Inokentijs Josts , Khedidja Mosbahi , Aleksander W. Roszak , Richard J. Cogdell , Alexandre M. J. J. Bonvin , Joel J. Milner , Sharon M. Kelly , Olwyn Byron , Brian O. Smith , Daniel Walker Nature Communications 7 DOI: 10.1038/ncomms13308 Diamond Proposal Number(s): [6638, 8659] Open Access Show Abstract ▼ Abstract: Iron is a limiting nutrient in bacterial infection putting it at the centre of an evolutionary arms race between host and pathogen. Gram-negative bacteria utilize TonB-dependent outer membrane receptors to obtain iron during infection. These receptors acquire iron either in concert with soluble iron-scavenging siderophores or through direct interaction and extraction from host proteins. Characterization of these receptors provides invaluable insight into pathogenesis. However, only a subset of virulence-related TonB-dependent receptors have been currently described. Here we report the discovery of FusA, a new class of TonB-dependent receptor, which is utilized by phytopathogenic Pectobacterium spp. to obtain iron from plant ferredoxin. Through the crystal structure of FusA we show that binding of ferredoxin occurs through specialized extracellular loops that form extensive interactions with ferredoxin. The function of FusA and the presence of homologues in clinically important pathogens suggests that small iron-containing proteins represent an iron source for bacterial pathogens. DOI: 10.1038/ncomms13308 OPEN 1	Oct 2016
I02-Macromolecular Crystallography I03-Macromolecular Crystallography I04-Macromolecular Crystallography	Structures of the ultra-high-affinity protein–protein complexes of pyocins S2 and AP41 and their cognate immunity proteins from Pseudomonas aeruginosa Amar Joshi , Rhys Grinter , Inokentijs Josts , Sabrina Chen , Justyna Wojdyla , Edward D. Lowe , Renata Kaminska , Connor Sharp , Laura Mccaughey , Aleksander Roszak , Richard J. Cogdell , Olwyn Byron , Daniel Walker , Colin Kleanthous Journal Of Molecular Biology 427 (17), 2852 - 2866 DOI: 10.1016/j.jmb.2015.07.014 PMID: 26215615 Diamond Proposal Number(s): [9306, 6638, 8659] Open Access Show Abstract ▼ Abstract: How ultra-high-affinity protein protein interactions retain high specificity is still poorly understood. The interaction between colicin DNase domains and their inhibitory immunity (Im) proteins is an ultra-high-affinity interaction that is essential for the neutralisation of endogenous DNase catalytic activity and for protection against exogenous DNase bacteriocins. The colicin DNase-Im interaction is a model system for the study of high-affinity protein protein interactions. However, despite the fact that closely related colicin-like bacteriocins are widely produced by Gram-negative bacteria, this interaction has only been studied using colicins from Escherichia coli. In this work, we present the first crystal structures of two pyocin DNase-Im complexes from Pseudomonas aeruginosa, pyocin S2 DNase-ImS2 and pyocin AP41 DNase-ImAP41. These structures represent divergent DNase Im subfamilies and are important in extending our understanding of protein protein interactions for this important class of high-affinity protein complex. A key finding of this work is that mutations within the immunity protein binding energy hotspot, helix III, are tolerated by complementary substitutions at the DNase Immunity protein binding interface. Im helix III is strictly conserved in colicins where an Asp forms polar interactions with the DNase backbone. ImAP41 contains an Asp-to-Gly substitution in helix III and our structures show the role of a co-evolved substitution where Pro in DNase loop 4 occupies the volume vacated and removes the unfulfilled hydrogen bond. We observe the co-evolved mutations in other DNase Immunity pairs that appear to underpin the split of this family into two distinct groups. (C) 2015 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).	Aug 2015
I02-Macromolecular Crystallography I03-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Structure of protease-cleaved Escherichia coli alpha-2-macroglobulin reveals a putative mechanism of conformational activation for protease entrapment Cameron Fyfe , Rhys Grinter , Inokentijs Josts , Khedidja Mosbahi , Aleksander Roszak , Richard J. Cogdell , Daniel M. Wall , Richard J. S. Burchmore , Olwyn Byron , Daniel Walker Acta Crystallographica Section D Biological Crystallography 71 (7), 1478 - 1486 DOI: 10.1107/S1399004715008548 PMID: 26143919 Diamond Proposal Number(s): [8659] Open Access Show Abstract ▼ Abstract: Bacterial alpha-2-macroglobulins have been suggested to function in defence as broad-spectrum inhibitors of host proteases that breach the outer membrane. Here, the X-ray structure of protease-cleaved Escherichia coli alpha-2-macroglobulin is described, which reveals a putative mechanism of activation and conformational change essential for protease inhibition. In this competitive mechanism, protease cleavage of the bait-region domain results in the untethering of an intrinsically disordered region of this domain which disrupts native interdomain interactions that maintain E. coli alpha-2-macroglobulin in the inactivated form. The resulting global conformational change results in entrapment of the protease and activation of the thioester bond that covalently links to the attacking protease. Owing to the similarity in structure and domain architecture of Escherichia coli alpha-2-macroglobulin and human alpha-2-macroglobulin, this protease-activation mechanism is likely to operate across the diverse members of this group.	Jul 2015
I03-Macromolecular Crystallography	Recombinant expression, purification, crystallization and preliminary X-ray diffraction analysis of the C-terminal DUF490 (963-1138) domain of TamB from Escherichia coli Inokentijs Josts , Rhys Grinter , Sharon Kelly , Khedidja Mosbahi , Aleksander Roszak , Richard J. Cogdell , Brian O. Smith , Olwyn Byron , Daniel Walker Acta Crystallographica Section F Structural Biology Communications 70, 1272 - 1275 DOI: 10.1107/S2053230X14017403 PMID: 25195908 Diamond Proposal Number(s): [5689] Show Abstract ▼ Abstract: TamB is a recently described inner membrane protein that, together with its partner protein TamA, is required for the efficient secretion of a subset of autotransporter proteins in Gram-negative bacteria. In this study, the C-terminal DUF490963–1138 domain of TamB was overexpressed in Escherichia coli K-12, purified and crystallized using the sitting-drop vapour-diffusion method. The crystals belonged to the primitive trigonal space group P3121, with unit-cell parameters a = b = 57.34, c = 220.74 Å, and diffracted to 2.1 Å resolution. Preliminary secondary-structure and X-ray diffraction analyses are reported. Two molecules are predicted to be present in the asymmetric unit. Experimental phasing using selenomethionine-labelled protein will be undertaken in the future.	Sep 2014
I02-Macromolecular Crystallography I03-Macromolecular Crystallography	Structure of the atypical bacteriocin pectocin M2 implies a novel mechanism of protein uptake Rhys Grinter , Inokentijs Josts , Kornelius Zeth , Aleksander Roszak , Laura C. Mccaughey , Richard J. Cogdell , Joel J. Milner , Sharon Kelly , Olwyn Byron , Daniel Walker Molecular Microbiology 93 (2), 234 - 246 DOI: 10.1111/mmi.12655 PMID: 24865810 Diamond Proposal Number(s): [6638, 8659] Open Access Show Abstract ▼ Abstract: The colicin-like bacteriocins are potent protein antibiotics that have evolved to efficiently cross the outer membrane of Gram-negative bacteria by parasitizing nutrient uptake systems. We have structurally characterized the colicin M-like bacteriocin, pectocin M2, which is active against strains of Pectobacterium spp. This unusual bacteriocin lacks the intrinsically unstructured translocation domain that usually mediates translocation of these bacteriocins across the outer membrane, containing only a single globular ferredoxin domain connected to its cytotoxic domain by a flexible α-helix, which allows it to adopt two distinct conformations in solution. The ferredoxin domain of pectocin M2 is homologous to plant ferredoxins and allows pectocin M2 to parasitize a system utilized by Pectobacterium to obtain iron during infection of plants. Furthermore, we identify a novel ferredoxin-containing bacteriocin pectocin P, which possesses a cytotoxic domain homologous to lysozyme, illustrating that the ferredoxin domain acts as a generic delivery module for cytotoxic domains in Pectobacterium.	Jul 2014
I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Lectin-like bacteriocins from Pseudomonas spp. utilise D-rhamnose containing lipopolysaccharide as a cellular receptor Laura C. Mccaughey , Rhys Grinter , Inokentijs Josts , Aleksander Roszak , Kai I. Waløen , Richard J. Cogdell , Joel Milner , Tom Evans , Sharon Kelly , Nicholas P. Tucker , Olwyn Byron , Brian Smith , Daniel Walker Plos Pathogens 10 (2) DOI: 10.1371/journal.ppat.1003898 PMID: 24516380 Diamond Proposal Number(s): [6683] Open Access Show Abstract ▼ Abstract: Lectin-like bacteriocins consist of tandem monocot mannose-binding domains and display a genus-specific killing activity. Here we show that pyocin L1, a novel member of this family from Pseudomonas aeruginosa, targets susceptible strains of this species through recognition of the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide that is predominantly a homopolymer of d-rhamnose. Structural and biophysical analyses show that recognition of CPA occurs through the C-terminal carbohydrate-binding domain of pyocin L1 and that this interaction is a prerequisite for bactericidal activity. Further to this, we show that the previously described lectin-like bacteriocin putidacin L1 shows a similar carbohydrate-binding specificity, indicating that oligosaccharides containing d-rhamnose and not d-mannose, as was previously thought, are the physiologically relevant ligands for this group of bacteriocins. The widespread inclusion of d-rhamnose in the lipopolysaccharide of members of the genus Pseudomonas explains the unusual genus-specific activity of the lectin-like bacteriocins.	Feb 2014
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	The crystal structure of the lipid II-degrading bacteriocin syringacin M suggests unexpected evolutionary relationships between colicin M-like bacteriocins Rhys Grinter , A Roszak , R. J. Cogdell , J. J. Milner , D. Walker Journal Of Biological Chemistry DOI: 10.1074/jbc.M112.400150 PMID: 22995910 Diamond Proposal Number(s): [6683] Open Access Show Abstract ▼ Abstract: Colicin-like bacteriocins show potential as next generation antibiotics with clinical and agricultural applications. Key to these potential applications is their high potency and species specificity that enables a single pathogenic species to be targeted with minimal disturbance of the wider microbial community. Here we present the structure and function of the colicin M-like bacteriocin, syringacin M from Pseudomonas syringae pv. tomato DC3000. Syringacin M kills susceptible cells through a highly specific phosphatase activity that targets lipid II, ultimately inhibiting peptidoglycan synthesis. Comparison of the structures of syringacin M and colicin M reveals that, in addition to the expected similarity between the homologous C-terminal catalytic domains, the receptor binding domains of these proteins, which share no discernible sequence homology, share a striking structural similarity. This indicates that the generation of the novel receptor binding and species specificities of these bacteriocins has been driven by diversifying selection rather than diversifying recombination as suggested previously. Additionally, the structure of syringacin M reveals the presence of an active site calcium ion that is coordinated by a conserved aspartic acid side chain and is essential for catalytic activity. We show that mutation of this residue to alanine inactivates syringacin M and that the metal ion is absent from the structure of the mutant protein. Consistent with the presence of Ca2+ in the active site, we show that syringacin M activity is supported by Ca2+, along with Mg2+ and Mn2+, and the protein is catalytically inactive in the absence of these ions.	Sep 2012

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