Biology subjects

Le Roy, A.

Publications and source records attributed to Le Roy, A..

7 recordsLinked to original sources

bioRxiv2026

Interlaboratory benchmarking of differential scanning fluorimetry reveals sources of variability in protein thermal stability parameters

Differential scanning fluorimetry (DSF) is widely used to assess protein thermal stability and to compare protein variants, ligands, or formulations with limited sample consumption. Yet, the reproducibility of DSF derived parameters across laboratories, instruments and analysis workflows remains poorly defined. Here, we report a two phase interlaboratory benchmark using a shared VHH sample across 26 laboratories, 28 instruments and seven DSF instrument models. In Phase 1, participants applied their routine acquisition and analysis workflows, whereas in Phase 2, acquisition conditions were harmonised. Datasets were analysed locally and then centrally reprocessed with MoltenProt. Participant reported apparent melting temperatures (Tm) showed good within instrument repeatability but moderate inter instrument dispersion. Harmonisation of acquisition conditions did not substantially reduce this dispersion. Conversely, centralised reprocessing narrowed the distribution among retained datasets, indicating contributions from analysis workflows and data acceptance criteria in addition to instrument dependent factors. Comparison with differential scanning calorimetry (DSC) further showed that apparent Tm depended strongly on the fluorescence readout. For this VHH, single wavelength fluorescence at 350 nm showed the closest agreement with the DSC transition temperature, whereas the 350/330 nm ratio and barycentric mean generally yielded higher values. Furthermore, DSF derived apparent unfolding enthalpies were more variable than apparent Tm. Together, these findings show that DSF can be highly repeatable within a defined instrument and workflow, but that quantitative comparability across instruments depends on instrument specific effects, the choice of fluorescence readout and analysis strategy. Improved comparability will require transparent reporting of acquisition and analysis conditions, explicit data quality criteria, and well characterised reference materials to monitor instrument dependent offsets.

biophysics↗

bioRxiv2026

Structural modelling and functional analysis support lipid binding by the dimeric E. coli DedA protein YqjA

Maintenance of membrane homeostasis is essential for bacterial viability, yet the molecular functions of many membrane proteins involved in this process remain poorly understood. The widely distributed DedA superfamily of integral membrane proteins has been implicated in membrane homeostasis, with deletion of DedA genes resulting in sensitivities to temperature, pH and a range of antimicrobial compounds. Several bacterial DedA proteins have been linked to lipid transport, providing a potential connection between function and phenotype. However, a lack of direct functional and structural data means that the precise role of DedA proteins in bacterial membrane homeostasis remains unclear. Here, using analytical ultracentrifugation (AUC), we show that the Escherichia coli DedA protein YqjA exists predominantly as a dimer and, by combining structural modelling with site-specific cysteine crosslinking, we have identified the most likely dimer interface. Modelling of dimeric YqjA in the presence of lipids predicts an interfacial lipid-binding site located in close proximity to several conserved, functionally important residues. Consistent with lipid binding, addition of lipid substantially increased the thermal stability of YqjA. Furthermore, mutation of residues associated with the predicted binding site impaired YqjA function. Together, these findings provide new structural and functional insights into the DedA family and support a role for lipid binding in the activity of YqjA.

biochemistry↗

bioRxiv2026

Superinfection exclusion strategy of siphophage T5: analysis of the FhuA:Llp complex

Superinfection exclusion is a widespread viral mechanism that protects the infected cell from over infection by other, identical or closely related viruses. Shortly after infection by bac-teriophage T5, the bacterium E. coli produces Llp coded by the just injected viral genome. Llp is a small lipoprotein targeted to the inner-leaflet of the host outer-membrane. It binds to FhuA, an outer-membrane iron-ferrichrome transporter, which is T5 receptor at the E. coli cell surface. The interaction between Llp and FhuA prevents any further bacteriophage binding and infection. Here, we determined the RMN structure of Llp and analyse the formation of the FhuA:Llp complex using a wide range of techniques and mutants, both in vivo and in vitro. Interaction of Llp to FhuA is governed by a two-step equilibrium with a strong contribution of induced fit: Llp binding requires remodelling of FhuA periplasmic plug surface, allowing the further large conformational reorganisation of the extracellular loops. Analysis of FhuA mu-tants show the importance of the intertwined interactions between the extracellular loops and the plug in the communication between the periplasmic and the extracellular faces of FhuA.

biophysics↗

bioRxiv2025

Analytical Ultracentrifugation as a Tool for Exploring COSAN Assemblies.

The self-assembly of the cobalta bis(dicarbollide) (COSAN) anionic boron clusters into micelles above a critical micelle concentration (cmc) of 10 - 20 mM and its behavior as "sticky nano-ions" facilitating controlled protein aggregation have been previously investigated using scattering techniques, particularly small-angle neutron and X-ray scattering. These techniques effectively provide average structural parameters but, when applied to colloidal systems, often rely on models assuming polydispersity or anisotropic shapes. Thus, complementary techniques are required to confirm or infirm the proposed analyses. Here, we employed sedimentation velocity analytical ultracentrifugation (SV-AUC), which offers the ability to resolve discrete species. We revisited two key questions: (1) the aggregation behavior of COSAN into micelles, a topic still under debate and due to its unconventional amphiphilic nature, and (2) the nature of the protein assemblies induced by COSAN, specifically their size/shape distribution and aggregation number. Our findings confirm the cmc of COSAN of 16 mM and reveal that COSAN micelles exhibit low aggregation numbers (8 in water and 14 in dilute salt), consistent with recent hypotheses. Furthermore, SV-AUC showed that COSAN promotes myoglobin aggregation into discrete oligomeric species with well-defined aggregation numbers, such as dimers, tetramers, and higher-order assemblies, depending on the COSAN-to-protein ratio. These results provide clarity on the discrete nature of COSAN micelle aggregation and protein assembly. This study highlights the complementary role of SV-AUC in understanding supramolecular assemblies, offering useful insights into the behavior of COSAN nano-ions and their interactions with biomacromolecules.

biophysics↗

bioRxiv2023

Targeting BTN2A1 enhances Vγ9Vδ2 T cell effector functions and triggers tumor cells pyroptosis

V{gamma}9V{delta}2 T cells are potent but elusive cytotoxic effectors. Means to stimulate their function could lead to powerful new cancer immunotherapies. BTN2A1, a surface protein has recently been shown to bind the V{gamma}9 chain of the {gamma}{delta} TCR but its precise role in modulating V{gamma}9V{delta}2 T cells functions remains unknown. Here we show that 107G3B5, a monoclonal anti-BTN2A1 agonist antibody, significantly enhances V{gamma}9V{delta}2 T cell functions against hematological or solid cell lines and against primary cells from adult acute lymphoblastic leukemia patients. New computer vision strategies applied to holotomographic microscopy videos show that 107G3B5 enhances the interaction between V{gamma}9V{delta}2 T cells and target cells in a quantitative and qualitative manner. In addition, we provide evidence that V{gamma}9V{delta}2 T cells activated by 107G3B5 induce caspase 3/7 activation in tumor cells, thereby triggering their death by pyroptosis. We thus demonstrate that targeting BTN2A1 with 107G3B5 enhances the V{gamma}9V{delta}2 T cell antitumor response by triggering the pyroptosis-induced immunogenic cell death.

cancer biology↗

bioRxiv2023

Characterization of the REC114-MEI4-IHO1 complex regulating meiotic DNA double-strand break formation

Meiotic recombination is initiated by the formation of DNA double-strand breaks (DSBs), essential for fertility and genetic diversity. In the mouse, DSBs are formed by the catalytic TOPOVIL complex consisting of SPO11 and TOPOVIBL. To preserve genome integrity, the activity of the TOPOVIL complex is finely controlled by several meiotic factors including REC114, MEI4 and IHO1, but the underlying mechanism is poorly understood. Here, we report that mouse REC114 forms homodimers, that it associates with MEI4 as a 2:1 heterotrimer that further dimerizes, and that IHO1 forms coiled-coil based tetramers. Using AlphaFold2 modelling combined with biochemical characterization we uncovered the molecular details of these assemblies. Finally, we show that IHO1 directly interacts with the PH domain of REC114 by recognizing the same surface as TOPOVIBL and another meiotic factor ANKRD31. These results provide strong evidence for the existence of a ternary IHO1-REC114-MEI4 complex and show that REC114 is a potential regulatory platform mediating mutually exclusive interactions with several partners.

biochemistry↗

bioRxiv2021

Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction

Deinococcus radiodurans is a spherical bacterium well-known for its outstanding resistance to DNA-damaging agents. Exposure to such agents leads to drastic changes in the transcriptome of D. radiodurans. In particular, four Deinococcus-specific genes, known as DNA Damage Response genes, are strongly up-regulated and have been shown to contribute to the resistance phenotype of D. radiodurans. One of these, DdrC, is expressed shortly after exposure to {gamma}-radiation and is rapidly recruited to the nucleoid. In vitro, DdrC has been shown to compact circular DNA, circularize linear DNA, anneal complementary DNA strands and protect DNA from nucleases. To shed light on the possible functions of DdrC in D. radiodurans, we determined the crystal structure of the domain-swapped DdrC dimer at a resolution of 2.2 [A] and further characterized its DNA binding and compaction properties. Notably, we show that DdrC bears two asymmetric DNA binding sites located on either side of the dimer and can modulate the topology and level of compaction of circular DNA. These findings suggest that DdrC may be a DNA damage-induced nucleoid-associated protein that enhances nucleoid compaction to limit the dispersion of the fragmented genome and facilitate DNA repair after exposure to severe DNA damaging conditions.

microbiology↗