B21-High Throughput SAXS
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Diamond Proposal Number(s):
[31850]
Open Access
Abstract: To ensure safety, pharmaceuticals are rigorously tested for lipopolysaccharide (LPS) contamination, as this can trigger severe immune reactions in patients. Low Endotoxin Recovery (LER), describing the masking of spiked LPS controls in Limulus Amebocyte Lysate (LAL) assays, has been associated with the presence of chelating agents and surfactants in pharmaceutical formulations. The addition of excipients, such as Mg2+, have shown the ability to mitigate the effects of LER, however, inconsistencies in various studies regarding the influence of the excipients on LPS aggregate characteristics and LER occurrence hinder a clear understanding of the mechanisms underlying LER. In this study, dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) were employed to systematically assess the impact of chelating agents, surfactants, and divalent cations on the size and shape of LPS aggregates across various formulations. Our results indicate that surfactant-only formulations generally reduce LPS aggregate size, whereas chelating agent-only formulations do not. Notably, the smallest aggregates were observed when both chelating agents and surfactants were present, with the extent of size reduction being specific to the particular excipients used. Additionally, Mg2+ generally inhibited the excipients’ capacity to decrease aggregate size, most effectively in phosphate-containing samples. Despite these variations in size, the overall aggregate shape remained largely unchanged in all formulations. These findings suggest that LPS aggregate size or shape does not distinguish formulations causing LER; instead, factors such as the characteristics of the LPS aggregate surface in different formulations should be explored in the future.
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Nov 2025
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[31378]
Open Access
Abstract: Amphiphilic compounds, such as phospholipids or surface-active substances, are present in biological systems and can be part of pharmaceutical formulations. As a consequence, all pharmaceutically active ingredients will encounter amphiphilic compounds, either in the formulation or after administration. With the growing interest in peptide-based pharmaceuticals, there is a need to enhance the understanding of the interactions between peptides and amphiphilic compounds.
In this particular study, we have chosen to study mixtures of the comparatively small cyclical octapeptide lanreotide and the conventional anionic surfactant sodium dodecylsulfate (SDS). This was done by examining the self-assembly structures formed in lanreotide-SDS mixtures using light scattering and small-angle X-ray scattering (SAXS).
Above the critical micelle concentration (cmc) of SDS, the large excess of SDS could solubilize all lanreotide and form small micelles with lanreotide attached to the interface. Upon dilution to concentrations below the cmc of SDS, a suspension with dispersed solid nanoparticles is formed. The solid nanoparticles grow in size with decreasing concentration and, eventually, precipitate. The precipitated material is arranged in a liquid crystalline micellar phase, consisting of small close-packed SDS micelles with peptide adsorbed at the interface.
We were able to conclude that lanreotide does not form mixed micelles with SDS, indicating that it lacks the amphiphilic properties required to integrate fully with SDS behaving as a cosurfactant. In contrast, lanreotide attaches to the interface of SDS micelles, resembling the interactions of polymers, proteins, and nucleic acids with surfactants.
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Nov 2025
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E01-JEM ARM 200CF
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Diamond Proposal Number(s):
[35899]
Open Access
Abstract: Encapsulins are microbial protein nanocompartments that spatially organize and sequester specific biochemical processes, including iron storage. While their protein shells have been extensively characterized, the composition and structure of their mineral cores remain less understood. Here, we use bright field transmission electron microscopy (BF TEM), high-angle annular dark-field scanning TEM (HAADF STEM), energy-dispersive X-ray (EDX), and electron energy-loss spectroscopy (EELS) in STEM to characterize the iron-containing mineral granules within the Myxococcus xanthus encapsulin system at near atomic resolution. We find that the internal nanoparticles are smaller (~2 nm) and more numerous (up to ~2200 per encapsulin) than previously reported. These nanoparticles are typically amorphous and have a composition consistent with FePO4 (measured Fe:P ratio of ≈1:1.2). Each encapsulin contains on average ~8500 iron atoms, corresponding to a volumetric density of 2.1 atoms/nm3. Phosphorus incorporation inhibits crystallization, whereas growth in phosphorus-free media leads to the formation of nano-crystalline goethite [α-FeO(OH)].
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Nov 2025
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I03-Macromolecular Crystallography
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Cholpon
Tilegenova
,
Tun
Liu
,
Qian
Zhao
,
Mahati
Are
,
Yu
Zhao
,
Woo Suk
Choi
,
Anusarka
Bhaumik
,
Ruth
Steele
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Nicholas A.
Manieri
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Bengi
Turegun
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Alex
Ni
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Rosa M. F.
Cardoso
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Paul
Shaffer
,
Desmond
Clark
,
Robin
Ernst
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Wenyu
Li
,
Tracy
Taylor
,
Suresh Kumar
Swaminathan
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Bhargavi
Ramaraju
,
Kevin
Liaw
,
Steven A.
Jacobs
,
Sujata
Sharma
,
Wan Cheung
Cheung
,
Adam
Zwolak
Diamond Proposal Number(s):
[34711]
Abstract: Bispecific antibodies (bsAbs) can enable therapeutic mechanisms, such as dual antigen targeting or receptor agonism, that are impossible using monoclonal antibodies. BsAbs with IgG-like format (bsIgG) are comprised of two unique heavy chains, each having a cognate light chain. Co-expression of these four unique polypeptides often leads to several mispaired species that are difficult to separate from the target bsIgG due to their similar biophysical properties. Here we describe a set of mutations called ProAla that exploit a the unfolded protein response pathway of cells. ProAla heavy chains are engineered with higher folding energy barriers such that only the cognate light and heavy chains can induce folding, chaperone release and secretion. The structures of the ProAla Fab and Fc regions are identical in structure to normal antibodies, enabling maintenance of half-life and function. Mispaired polypeptides fail to secrete from the cell due to enhanced interaction with the endoplasmic reticulum chaperone BiP, resulting in increased purity of secreted bsIgGs.
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Oct 2025
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[34035]
Open Access
Abstract: Electron diffraction of 3D microcrystals (3D ED/MicroED) is an emerging technique that uses electrons to determine proteins structure from their nano-sized 3D crystals, thus overcoming the limitations on crystal-size dimensions generally imposed by X-ray or neutron diffraction. The strong interactions of electrons with matter have the potential to reveal the location of light atoms (e.g., hydrogens), revealing interaction networks, and to provide information about the charge states of the atoms. Recent advances in MicroED sample preparation and, data collection strategies, have led to structural determination of several known and unknown protein structures, including challenging targets such as membrane proteins. In this review we provide an overview of the recent advances of MicroED including sample preparation and data collection.
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Oct 2025
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I18-Microfocus Spectroscopy
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Diamond Proposal Number(s):
[35162]
Open Access
Abstract: Enamel erosion alters the structural integrity of the tooth surface, which can be measured using indentation techniques. However, traditional single-load indentation methods assume homogeneity within the eroded enamel, overlooking potential stratification within the subsurface lesion. This study investigates the presence of mechanical and porosity gradients within the enamel following simulated dietary acid exposure and examines how lesion depth and structure change with continued erosion. We applied varying-load micro-indentation to human enamel subjected to citric acid challenge, revealing a distinct stratification of mechanical properties. A soft superficial layer (~1- to 2-µm thick) exhibited significantly reduced hardness and was easily removed by ultrasonication, indicating its fragility. Beneath this layer, mechanical properties stabilized despite prolonged acid exposure (~3 min), suggesting a saturation point in lesion development. Profilometric analysis confirmed that although material loss increased with erosion time, the depth of the altered subsurface zone remained constant. To explore the porosity distribution, we used a novel gold nanoparticle labeling technique coupled with synchrotron-based X-ray fluorescence imaging. Nanoparticles (~20 nm) penetrated to depths of 15 to 20 µm, aligning closely with mechanical gradients inferred from indentation measurements. These findings indicate that subsurface enamel exhibits not only mechanical stratification but also corresponding variations in porosity. Our results demonstrate the limitations of single-load indentation in characterizing erosion-affected enamel and highlight the utility of multiload approaches in detecting structural heterogeneity. The correlation between mechanical softening and increased porosity suggests that the enamel subsurfaces are differentially affected. These findings raise important implications for therapeutic intervention: should remineralization strategies shift from bulk mineral delivery to layer-specific, functionally informed repair?
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Oct 2025
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I14-Hard X-ray Nanoprobe
I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[19466, 26220, 22709]
Open Access
Abstract: The deposition of calcium phosphate mineral within a collagen matrix plays a pivotal role in the formation of bone and teeth, yet understanding its precise mechanism and time-dependence remains a significant challenge. Conventional approaches are often constrained to ex situ studies and as a result the intrinsic dynamics governing collagen mineralization remains unclear. To address this knowledge gap, we developed a custom thermal flow cell to enable in situ characterization using Raman spectroscopy and small/wide-angle X-ray scattering for comparable sample settings. This approach allowed us to monitor the intricate process of collagen matrix mineralization from the initial infiltration of precursor phases to the formation of intermediate phosphate phases, and ultimately to the predominant growth of hydroxyapatite. Our findings reveal a striking expansion of the collagen matrix during initial infiltration, followed by compression in the early stages of mineralization, likely driven by water expulsion, which suggests the development of pre-stress similar to that observed in bone. As mineralization progressed, the matrix expanded once again, correlated with crystal growth. Post-mortem analyses confirmed the presence of intrafibrillar mineralization, with remarkable agreement to bone formation at up to 9 h of mineralization before over-mineralization occurred. Our study further identified a tessellated mineralization pattern within the collagen matrix, a feature also seen in bone, pointing to a highly regulated physico-chemical control of the mineralization dynamics. These insights deepen our understanding of the fundamental processes governing bone mineralization with broad implications for designing advanced biomaterials.
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Oct 2025
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Open Access
Abstract: Understanding the structure and dynamics of the hydrogen-bond network of water in topologically distinct swollen lipidic mesophases, is fundamental for their application in biomedical, pharmaceutical, and food science fields. Here, a positive and non-linear correlation between water hydrogen-bond dynamics and interfacial water population is uncovered in inverse bicontinuous swollen mesophases across an extended temperature range (298–340 K). Particularly, small-angle X-ray scattering determines the mesophase's structural features, uncovering a temperature-driven re-entrant phenomenon (reappearance) of
phase upon heating. This topologically rich environment, however, has no detectable impact on the temperature dependence of the intermolecular modes of water, as revealed by terahertz absorption spectroscopy. Specifically, these modes show distinct dynamics: the stretching mode exhibits longer lifetimes than the libration mode, yet with a higher temperature-dependence, with approximately two-fold lower Arrhenius activation energies. In contrast, both stretching and libration modes exhibit a monotonic decrease in lifetime with increasing temperature, due to the increasing disruption of the hydrogen-bond network. Atomistic molecular dynamics simulations enable the quantification of interfacial water population, which shows a positive correlation with intermolecular lifetimes in a nonlinear manner, revealing a non-additive coupling between interfacial water population and water hydrogen-bond network dynamics within these systems.
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Oct 2025
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I04-Macromolecular Crystallography
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Will
Scott
,
Esther
Ivorra-Molla
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Dipayan
Akhuli
,
Teresa
Massam-Wu
,
Pawel K.
Lysyganicz
,
Rylie
Walsh
,
Matthew
Parent
,
Jonathan
Cook
,
Lijiang
Song
,
Abhishek
Kumar
,
Falk
Schneider
,
Masanori
Mishima
,
Allister
Crow
,
Mohan K.
Balasubramanian
Open Access
Abstract: Photobleaching of fluorescent proteins often limits the acquisition of high-quality images in microscopy. StayGold, a novel dimeric green fluorescent protein recently monomerised through sequence engineering, addresses this challenge with its high photostability. There is now focus on producing different colour StayGold derivatives to facilitate concurrent tagging of multiple targets. The unnatural amino acid 3-aminotyrosine has previously been shown to red-shift superfolder GFP upon incorporation into its chromophore via genetic code expansion. Here we apply the same strategy to red-shift StayGold through substitution of Tyrosine-58 with 3-aminotyrosine. The resultant red fluorescent protein, StayRose, shows an excitation wavelength maximum of 530 nm and an emission wavelength maximum of 588 nm. Importantly, the monomeric mStayRose retains the favourable photostability in vivo in E. coli and zebrafish embryos. A high-resolution crystal structure of StayRose confirms the modified structure of the amino chromophore within an unperturbed 3D fold. Although reliant on genetic code expansion, StayRose provides an important step towards developing red-shifted StayGold derivatives.
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Oct 2025
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B23-Circular Dichroism
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Open Access
Abstract: The emergence of multidrug-resistant (MDR) bacterial pathogens is an alarming global health threat that demands new therapeutic strategies beyond conventional antibiotics. Here, we present a rationally designed antimicrobial peptide (AMP) derived from mammalian cathelicidins and defensins that selectively targets bacterial membranes with low cytotoxicity toward mammalian cells. Circular dichroism spectroscopy revealed that the peptide adopts an α-helical conformation upon membrane interaction, a key feature of its mechanism. Surface plasmon resonance and isothermal titration calorimetry demonstrated high-affinity and selective binding to bacterial lipid membranes. Functionally, the peptide was strongly bactericidal against clinical MDR Escherichia coli (E. coli) and clinically important ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.). Compared with the parent peptide LL-37, our AMP exhibited lower minimum inhibitory concentrations (MICs) and faster bactericidal kinetics across both Gram-negative and Gram-positive strains. Calcein leakage assays, showing effective membrane disruption. Importantly, cytotoxicity experiments with human epithelial (Caco-2) and immune (THP-1) cells indicated low cytotoxicity at concentrations exceeding bactericidal levels, supporting a favorable therapeutic window. ELISA quantifications of cytokines (IL-6, TNF-α) further suggested immunomodulatory effects at bactericidal concentrations. Transcriptomic profiling of E. coli treated with sub-lethal concentrations of the peptide exhibited upregulation of bacterial stress response pathways and downregulation of vital metabolic processes, reflecting the complex antimicrobial action of the peptide. Collectively, these findings highlight this LL-37-derived AMP as a promising candidate for treating MDR bacterial infections caused by E. coli and ESKAPE pathogens and for guiding the development of next-generation antimicrobial agents.
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Oct 2025
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