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Beatriz
Costa-Gomes
,
Joel
Greer
,
Nikolai
Juraschko
,
James
Parkhurst
,
Jola
Mirecka
,
Marjan
Famili
,
Camila
Rangel-Smith
,
Oliver
Strickson
,
Alan
Lowe
,
Mark
Basham
,
Tom
Burnley
Open Access
Abstract: Ease of access to data, tools and models expedites scientific research. In structural biology there are now numerous open repositories of experimental and simulated data sets. Being able to easily access and utilize these is crucial to allow researchers to make optimal use of their research effort. The tools presented here are useful for collating existing public cryoEM data sets and/or creating new synthetic cryoEM data sets to aid the development of novel data processing and interpretation algorithms. In recent years, structural biology has seen the development of a multitude of machine-learning-based algorithms to aid numerous steps in the processing and reconstruction of experimental data sets and the use of these approaches has become widespread. Developing such techniques in structural biology requires access to large data sets, which can be cumbersome to curate and unwieldy to make use of. In this paper, we present a suite of Python software packages, which we collectively refer to as PERC (profet, EMPIARreader and CAKED). These are designed to reduce the burden which data curation places upon structural biology research. The protein structure fetcher (profet) package allows users to conveniently download and cleave sequences or structures from the Protein Data Bank or AlphaFold databases. EMPIARreader allows lazy loading of Electron Microscopy Public Image Archive data sets in a machine-learning-compatible structure. The Class Aggregator for Key Electron-microscopy Data (CAKED) package is designed to seamlessly facilitate the training of machine-learning models on electron microscopy data, including electron-cryo-microscopy-specific data augmentation and labeling. These packages may be utilized independently or as building blocks in workflows. All are available in open-source repositories and designed to be easily extensible to facilitate more advanced workflows if required.
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Oct 2025
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I03-Macromolecular Crystallography
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Emily C.
Hank
,
Nicholas D.
D'Arcy-Evans
,
Emma R.
Scaletti
,
Carlos
Benítez-Buelga
,
Olov
Wallner
,
Florian
Ortis
,
Kaixin
Zhou
,
Liuzhen
Meng
,
Alicia
Del Prado
,
Patricia
Calvo
,
Ingrid
Almlöf
,
Elisée
Wiita
,
Karen
Nierlin
,
Sara
Kosenina
,
Andreas
Krämer
,
Alice
Eddershaw
,
Mario
Kehler
,
Maeve
Long
,
Ann-Sofie
Jemth
,
Holly
Dawson
,
Josephine
Stewart
,
Adam
Dickey
,
Mikhael E.
Astorga
,
Marek
Varga
,
Evert J.
Homan
,
Martin
Scobie
,
Stefan
Knapp
,
Leandro
Sastre
,
Pal
Stenmark
,
Miguel
De Vega
,
Thomas
Helleday
,
Maurice
Michel
Diamond Proposal Number(s):
[15806, 21625]
Open Access
Abstract: Bifunctional DNA glycosylases employ an active site lysine or the N-terminus to form a Schiff base with an abasic (AP) site base excision repair intermediate. For 8-oxoguanine DNA glycosylase 1 (OGG1), cleaving this reversible structure is the rate-determining step in the initiation of 8-oxoguanine (8-oxoG) repair in DNA. Evolution has led OGG1 to use a product-assisted catalysis approach, where the excised 8-oxoG acts as a Brønsted base for cleavage of a Schiff base intermediate. However, the physicochemical properties of 8-oxoG significantly limit the inherent enzymatic turnover leading to a weak, cellularly absent, AP lyase activity. We hypothesized that chemical synthesis of purine analogues enables access to complex structures that are suitable as product-like catalysts. Herein, the nucleobase landscape is profiled for its potential to increase OGG1 Schiff base cleavage. 8-Substituted 6-thioguanines emerge as potent and selective scaffolds enabling OGG1 to cleave AP sites opposite any canonical nucleobase by β-elimination. This effectively broadens the enzymatic substrate scope of OGG1, shaping a complete, artificial AP-lyase function. In addition, a second class of compounds, 6-substituted pyrazolo-[3,4-d]-pyrimidines, stimulate OGG1 function at high pH, while thioguanines govern enzymatic control at acidic pH. This enables up to 20-fold increased enzyme turnover and a de novo OGG1 β-elimination in conditions commonly not tolerated. The tool compounds employed here are non-toxic in cells and stimulate the repair of AP sites through a natural, APE1 dependent pathway, as opposed to previously reported β,δ-lyase stimulator TH10785.
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Oct 2025
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B21-High Throughput SAXS
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Cassandra R.
Kennedy
,
Katherine A.
Mcphie
,
Aini
Vuorinen
,
Jane
Dudley-Fraser
,
Diego
Esposito
,
Sarah
Maslen
,
William J.
Mccarthy
,
Jonathan
Pettinger
,
J. Mark
Skehel
,
David
House
,
Katrin
Rittinger
,
Jacob
Bush
Diamond Proposal Number(s):
[32711]
Open Access
Abstract: As the global fight against antimicrobial resistance in bacteria becomes increasingly pressing, new tool compounds are needed to study and evaluate novel therapeutic targets. Here, cysteine-directed fragment-based drug discovery is coupled with high throughput chemistry direct-to-biology screening to target the catalytic cysteine of a family of bacterial effector proteins, the novel E3 ligases (NELs) from Salmonella and Shigella. These effector E3 ligases are attractive as potential drug targets because they are delivered into host cells during infection, have no human homologues and disrupt host immune response to infection. We successfully identify hit compounds against the SspH subfamily of NELs from Salmonella and show that these proteins are inhibited by compound treatment, representing an exciting starting point for development into specific and potent tool compounds.
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Oct 2025
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I02-Macromolecular Crystallography
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Open Access
Abstract: The trematode liver fluke Fasciola hepatica causes the neglected tropical disease fascioliasis in humans and is associated with significant losses in agricultural industry due to reduced animal productivity. Triosephosphate isomerase (TPI) is a glycolytic enzyme that has been researched as a drug target for various parasites, including F. hepatica. The high-resolution crystal structure of F. hepatica TPI (FhTPI) has been solved at 1.51 Å resolution in its monoclinic form. The structure has been used to perform molecular-docking studies with the most successful fasciolocide triclabendazole (TCBZ), which has recently been suggested to target FhTPI. Two FhTPI residues, Lys50 and Asp51, are located at the dimer interface and are found in close proximity to the docked TCBZ. These residues are not conserved in mammalian hosts.
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Sep 2025
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Krios IV-Titan Krios IV at Diamond
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Diamond Proposal Number(s):
[34130]
Open Access
Abstract: Branched actin networks nucleated by the Arp2/3 complex have critical roles in various cellular processes, from cell migration to intracellular transport. However, when activated by WISH/DIP/SPIN90-family proteins, Arp2/3 nucleates linear actin filaments. Here we found that human SPIN90 is a dimer that can nucleate bidirectional actin filaments. To understand the basis for this, we determined a 3-Å-resolution structure of human SPIN90–Arp2/3 complex nucleating actin filaments. Our structure shows that SPIN90 dimerizes through a three-helix bundle and interacts with two Arp2/3 complexes. Each SPIN90 molecule binds both Arp2/3 complexes to promote their activation. Our analysis demonstrates that single-filament nucleation by Arp2/3 is mechanistically more like branch formation than previously appreciated. The dimerization domain in SPIN90 orthologs is conserved in metazoans, suggesting that this mode of bidirectional nucleation is a common strategy to generate antiparallel actin filaments.
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Sep 2025
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Open Access
Abstract: As cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) continue to advance, the ability to visualize cellular and organismal structures with unprecedented clarity is redefining the landscape of structural biology. Breakthroughs in imaging technology, sample preparation and image processing now enable the detailed elucidation of cellular architecture, macromolecular organization, and dynamic biological processes at sub-nanometer resolution. Recent methodological advances have propelled the field to new frontiers, facilitating the investigation of complex biological questions across scales—from macromolecular complexes to organism-wide structural insights. This review explores rapidly emerging trends, highlights key innovations that are pushing the boundaries of in situ structural biology, and addresses persistent challenges in expanding the applicability of cryo-EM and cryo-ET across diverse biological systems.
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Aug 2025
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[28516]
Abstract: Mutations in the E3 ubiquitin ligase Parkin gene have been linked to early onset Parkinson’s disease. Besides many other roles, Parkin is involved in clearance of damaged mitochondria via mitophagy—a process of particular importance in dopaminergic neurons. Upon mitochondrial damage, Parkin accumulates at the outer mitochondrial membrane and is activated, leading to ubiquitination of many mitochondrial substrates and recruitment of mitophagy effectors. While the activation mechanisms of autoinhibited Parkin have been extensively studied, it remains unknown how Parkin recognizes its substrates for ubiquitination. Here, we characterize a conserved region in the flexible linker between the Ubl and RING0 domains of Parkin, which is indispensable for Parkin interaction with the mitochondrial GTPase Miro1. Our results may explain fast kinetics of Miro1 ubiquitination by Parkin in recombinant assays and provide a biochemical explanation for Miro1-dependent Parkin recruitment to the mitochondrial membrane observed in cells. Our findings are important for understanding mitochondrial homeostasis and may inspire new therapeutic avenues for Parkinson’s disease.
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Aug 2025
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[25413]
Open Access
Abstract: Analysis of ligand-induced structural changes in proteins is challenging due to the lack of experimental methods suited for detection and characterisation of both ligand binding and induced structural changes. We have explored biosensors with different detection principles to study interactions between ligands and acetylcholine binding proteins (AChBPs), soluble homologues of Cys-loop ligand gated ion channels (LGICs) that undergo similar structural changes as LGICs upon ligand binding. X-ray crystallography was used to identify binding sites and establish if detected conformational changes involved small changes in loop C or major structural changes in the pentamer associated with ion channel opening. Experiments were initially focused on ligands exhibiting complex Surface Plasmon Resonance (SPR) biosensor sensorgrams or that were detected by Second Harmonic Generation (SHG) biosensor analysis. Surface Acoustic Wave (SAW) and SHG biosensors confirmed that complexities in SPR data were indeed due to ligand-induced conformational changes. Grating Coupled Interferometry (GCI) biosensor sensorgrams were less complex, despite similar detection principles. switchSENSE biosensor analysis revealed that ligands resulted in either a compaction or expansion of the protein structure. The X-ray crystallography of the protein-ligand complexes was only successful for 7 out of 12 ligands, despite nM-µM affinities. Crystals were not obtained for the two compounds shown by SHG analysis to induce large structural changes, while electron densities were not seen in the structures for some ligands. The work presented herein has shown that several biosensor technologies have a unique capability to detect and discriminate binding and ligand induced conformational changes in proteins, also when interactions are rapid, weak and structural changes small. However, they are complementary and give different information.
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Aug 2025
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[23459]
Open Access
Abstract: Following its deorphanisation in the early 2000s, the farnesoid X receptor (FXR) attracted significant attention for regulating genes involved in bile acid, lipid and glucose metabolism and inflammation, pathways central to many liver diseases. As such, pharmaceutical efforts targeted FXR for their treatment. However, while FXR agonists, such as obeticholic acid, have been studied in clinical trials, many were associated with adverse effects arising from the promiscuity of systemic FXR activation, thus efforts to limit or selectively modulate the downstream effects of FXR are crucially important. In work here, two novel bile acid derivatives, previously identified via molecular docking and cell-based screening, were validated by X-ray crystallography and tested in LanthaScreen coactivator recruitment assays. Their effects on downstream FXR signalling were assessed in vitro in hepatocellular carcinoma cells, and in vivo in C57BL/6 mice, by RNA sequencing and RT-qPCR. The novel compounds exhibited potent and selective FXR agonist activity. Co-crystal structures of FXR LBD with both compounds, demonstrated distinctive binding modes for each, including occupancy of a receptor sub-pocket associated with allosteric activation, not observed with classic bile acids. Both compounds were up to four-fold more potent than obeticholic acid and demonstrated ligand-dependent differences in coactivator recruitment assays. In vitro, both compounds induced greater changes in the expression of FXR target genes, at lower doses than obeticholic acid. In vivo, compound-dependent differential gene expression was observed. These findings suggest that the novel compounds may enable gene-specific FXR regulation through differential coactivator usage and hold potential to overcome the shortcomings of current bile acid drugs, thus representing promising candidates for further research.
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Aug 2025
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Abstract: Hepatoma-derived growth factor-related protein 2 (HRP-2) is a member of the HDGF-related protein family, which has been linked to multiple malignancies. A defining feature of this protein family is the presence of an N-terminal PWWP domain, which enables binding to nucleosomes carrying a dimethylation or trimethylation marker on residue Lys36 of histone H3. To support the rational design of small-molecule drugs that bind to the PWWP domain, crystallographic fragment screening was chosen. A critical requirement for such screening is the ability to reliably produce large batches of high-quality crystals, ideally grown under low-salt conditions to prevent the precipitation of drug-like fragments during crystal soaking. Initial crystallization of the wild-type (WT) HRP-2 PWWP domain only produced crystals under high-salt conditions and these significantly lost diffraction quality over two weeks. It was hypothesized that these complications were caused by oxidation of the solvent-exposed Cys64 residue. To overcome these difficulties, a Cys64Ser mutant was produced. This mutation revealed a substantially improved crystallization propensity, as eight crystal forms could be obtained and resolved versus two forms for the WT. Moreover, the mutant crystals could be grown in PEG-based low ionic strength conditions which are optimal for fragment soaking. Finally, the crystals did not lose their diffraction quality for up to six months. Importantly, systematic analysis of all obtained X-ray structures revealed that the Cys64/Ser64 residue lies at a key lattice interface which is conserved across all crystal forms. This suggests that even minor chemical changes at this position could disrupt important intermolecular contacts, explaining the demonstrated major benefit of the introduced mutation. The presented data underpin the substitution of surface-exposed cysteines as a general strategy to enhance protein crystallization and diffraction quality. Ultimately, the results presented here were pivotal to the successful execution of the crystallographic fragment-screening campaign with the HRP-2 PWWP domain.
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Aug 2025
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