Thomas Harry Sharp

Programming three-dimensional order in peptide-based materials requires lateral interactions that are precise enough to propagate over hundreds of nanometres, yet robust enough to operate in water. Here, we show that a rationally designed coiled-coil peptide meets both demands by assembling into a hierarchical suprahelix that promotes spontaneous crystallisation under physiological buffer conditions. Coiled-coil dimers wind around one another to generate the higher-order suprahelix. Subtle lysine-to-arginine substitutions tune lateral cohesion, revealing a non-monotonic dependence on arginine density: 46-residue peptides with three or six arginine residues form ellipsoidal nanocrystals, whereas arginine-free or arginine-rich variants form amorphous aggregates. Time-resolved spectroscopy and cryogenic electron microscopy show that crystallisation proceeds by a non-classical pathway, in which condensed protofibrils align before consolidating into an ordered lattice. Cryo-electron tomography supports the single-domain nature of the resulting nanocrystals, and three-dimensional electron diffraction shows that both crystalline variants adopt the same near hexagonal unit-cell metrics. These findings translate a principle from protein crystallography, that arginine favours crystal contacts relative to lysine, into a sequence-level design parameter for coiled-coil nanocrystallization, providing a route to programmable three-dimensional order in soft molecular materials.

Monoclonal antibodies are important modalities in the treatment of cancer. Post-translational modifications of proteins, such as glycosylation, can affect the binding affinity of therapeutic antibodies. Whether other PTMs modulate therapeutic antibody binding to different surface proteins is currently underexplored. Pyroglutamation is the post-translational cyclization of an N-terminal glutamine or glutamic acid residue into a pyroglutamate by glutaminyl cyclase. In this study, we investigated the impact of pyroglutamation on the binding affinity of three therapeutic antibodies targeting CD47 and TRP1. Here, we show that pyroglutamation on CD47 and TRP1 modulates the binding of anti(α)-CD47 magrolimab and αTRP1 TA99 and flanvotumab. Furthermore, the N-terminal glutamine on CD47 is crucial for effective antibody recognition, while pyroglutamation of TRP1 is involved in trafficking to the cell surface. These findings highlight that the pyroglutamation by glutaminyl cyclase can modulate the binding affinity of antibodies with therapeutic potential.

Immunoglobulin G (IgG) is a glycoprotein harboring conserved fragment crystallizable domain glycans, but it can also express variable domain glycans (VDGs). Elevated levels of VDGs are a hallmark of the autoantibodies most specific to rheumatoid arthritis and are also associated with other autoimmune diseases. Nonetheless, the effect of VDGs on IgG function remains poorly understood. This study investigates the impact of VDGs on the ability of antibodies to activate the complement system, a key immune effector mechanism. We demonstrate that VDGs on IgG inhibit the initiation of the classical complement pathway, as evidenced by complement activation assays with IgG displaying varying degrees of VDGs. Structure–function analyses show that VDGs reduce classical complement activation by impeding IgG oligomer formation on antigenic surfaces. As IgG oligomerization is essential for effective C1q binding, VDG-mediated interference with this process lowers IgG's complement activation potential. This impaired ability to recruit complement was further substantiated through direct visualization of IgG oligomer–C1q complexes on antigen-coated vesicles by cryoelectron tomography. Together, these data reveal that VDGs increase the functional diversity of IgG and identify a novel regulatory mechanism that modulates the ability of antibodies to activate one of their main immune effector mechanisms.

Clustering of type-II tumor necrosis factor receptors (TNFRs) is required to induce intracellular signaling. Current methods for receptor clustering lack precise control over ligand valency and spatial organization, potentially limiting optimal TNFR activation, biological insight, and therapeutic efficacy. DNA nanostructures provide nanometer-precise control over molecular arrangement, allowing control of both ligand spacing and valency. Here, we produce a DNA nanostructure decorated with controlled numbers of engineered single-chain TNF-related apoptosis-inducing ligand (sc-TRAIL) trimers, which bind death receptor 5 (DR5) with native affinity and geometry and enable investigation of the geometric parameters influencing apoptotic pathway activation. We show that cell killing is affected by receptor valency and separation and enhanced by superclustering sc-TRAIL trimers, which can induce cell killing in human primary pancreatic and colorectal cancer organoids. Together, our data show that control of receptor superclustering enhances our understanding of receptor activation mechanisms and informs the development of more effective cancer therapies.

Automation and improved hardware have greatly accelerated the rate of data generation in cryoET. As the field moves towards quantitative cryoET , the scale of the resulting datasets presents a significant challenge for analysis and interpretation. To explore ways of handling datasets comprising thousands of tomograms, we investigated a comprehensive segmentation strategy – assigning an ontology-based identity to every voxel in a dataset – that is based on the sequential application of multiple convolutional neural networks. Using an openly available dataset of over 1800 Chlamydomonas reinhardtii tomograms as a test case, we demonstrate the segmentation of 25 different subcellular features across the full dataset, while requiring only a few seconds of processing time per tomogram. We show how the approach enables the representation of large datasets as searchable databases and propose the usage of ontology-based segmentations for improving two common processing tasks in cryoET. First, we explore context-aware particle picking as a method to retain biological context when selecting particles for subtomogram averaging and other downstream analyses. Secondly, we demonstrate area-selective template matching , where we use segmentation-based masks to avoid redundant computations in template matching and enable >500-fold faster processing in specific cases. To illustrate the utility of the approach, all segmentation results have also been made available online via cryopom.streamlit.app .

Segmentation is a critical data processing step in many applications of cryo-electron tomography. Downstream analyses, such as subtomogram averaging, are often based on segmentation results, and are thus critically dependent on the availability of open-source software for accurate as well as high-throughput tomogram segmentation. There is a need for more user-friendly, flexible, and comprehensive segmentation software that offers an insightful overview of all steps involved in preparing automated segmentations. Here, we present Ais: a dedicated tomogram segmentation package that is geared towards both high performance and accessibility, available on GitHub. In this report, we demonstrate two common processing steps that can be greatly accelerated with Ais: particle picking for subtomogram averaging, and generating many-feature segmentations of cellular architecture based on in situ tomography data. Featuring comprehensive annotation, segmentation, and rendering functionality, as well as an open repository for trained models at aiscryoet.org, we hope that Ais will help accelerate research and dissemination of data involving cryoET.

Segmentation is a critical data processing step in many applications of cryo-electron tomography. Downstream analyses, such as subtomogram averaging, are often based on segmentation results, and are thus critically dependent on the availability of open-source software for accurate as well as high-throughput tomogram segmentation. There is a need for more user-friendly, flexible and comprehensive segmentation software that offers an insightful overview of all steps involved in preparing automated segmentations. Here, we present Ais: a dedicated tomogram segmentation package that is geared towards both high performance and accessibility, available at github.com/bionanopatterning/Ais. In this report, we demonstrate two common processing steps that can be greatly accelerated with Ais: particle picking for subtomogram averaging, and generating many-feature segmentations of cellular architecture based on in situ tomography data. Featuring comprehensive annotation, segmentation, and rendering functionality, as well as an open repository for trained models at aiscryoet.org, we hope that Ais will help accelerate research and dissemination of data involving cryoET.

Germline and somatic TP53 variants play a crucial role during tumorigenesis. However, genetic variations that solely affect the alternatively spliced p53 isoforms, p53β and p53γ, are not fully considered in the molecular diagnosis of Li-Fraumeni syndrome and cancer. In our search for additional cancer predisposing variants, we identify a heterozygous stop-lost variant affecting the p53β isoforms (p.*342Serext*17) in four families suspected of an autosomal dominant cancer syndrome with colorectal, breast and papillary thyroid cancers. The stop-lost variant leads to the 17 amino-acid extension of the p53β isoforms, which increases oligomerization to canonical p53α and dysregulates the expression of p53’s transcriptional targets. Our study reveals the capacity of p53β mutants to influence p53 signalling and contribute to the susceptibility of different cancer types. These findings underscore the significance of p53 isoforms and the necessity of comprehensive investigation into the entire TP53 gene in understanding cancer predisposition.

Human C-reactive protein (CRP) is a pentameric complex involved in immune defense and regulation of autoimmunity. CRP is also a therapeutic target, with both administration and depletion of serum CRP being pursued as a possible treatment for autoimmune and cardiovascular diseases, among others. CRP binds to phosphocholine (PC) moieties on membranes to activate the complement system via the C1 complex, but it is unknown how CRP, or any pentraxin, binds to C1. Here, we present a cryoelectron tomography (cryoET)-derived structure of CRP bound to PC ligands and the C1 complex. To gain control of CRP binding, a synthetic mimotope of PC was synthesized and used to decorate cell-mimetic liposome surfaces. Structure-guided mutagenesis of CRP yielded a fully active complex able to bind PC-coated liposomes that was ideal for cryoET and subtomogram averaging. In contrast to antibodies, which form Fc-mediated hexameric platforms to bind and activate the C1 complex, CRP formed rectangular platforms assembled from four laterally associated CRP pentamers that bind only four of the six available globular C1 head groups. Potential residues mediating lateral association of CRP were identified from interactions between unit cells in existing crystal structures, which rationalized previously unexplained mutagenesis data regarding CRP-mediated complement activation. The structure also enabled interpretation of existing biochemical data regarding interactions mediating C1 binding and identified additional residues for further mutagenesis studies. These structural data therefore provide a possible mechanism for regulation of complement by CRP, which limits complement progression and has consequences for how the innate immune system influences autoimmunity.