Biology subjects

Dehez, F.

Publications and source records attributed to Dehez, F..

13 recordsLinked to original sources

bioRxiv2026

Deinococcus radiodurans HU: a versatile architect of nucleoid structure and plasticity

Nucleoid-associated proteins are known to compact and organise bacterial genomes, but how their local DNA binding shapes higher-order chromatin architecture remains unclear. Using in vitro and in situ approaches, we investigated how Deinococcus radiodurans HU (DrHU) orchestrates nucleoid organisation. DrHU engages DNA through two synergistic binding modes: high-affinity {beta}-hairpin-mediated stabilisation of DNA loops and low-affinity, multivalent interaction via its N-terminal tail, driving parallel, uniformly spaced DNA alignment. In vitro, DrHU organises supercoiled plasmid DNA into regular 2D lattices of double-spirals, while in situ, UV-C light induces a nucleoid transition from a loose DNA mesh to a blue liquid crystalline phase characterised by DNA swirls. The striking structural similarity and shared inter-filament spacing of these two arrangements suggests that DrHU plays a pivotal role in genome organisation through its versatile binding properties that enable DNA loop stabilisation, protection and DNA bridging, linking molecular interactions to 3D genome ordering and stress-induced remodelling.

microbiology↗

bioRxiv2026

Structural basis of the two-photon photoactivation mechanism of orange carotenoid protein

Cyanobacteria have produced Earths oxygen for 2.4 billion years by adapting to fluctuating irradiance. This adaptation relies on orange carotenoid protein (OCP), which mediates light-intensity- dependent photoprotective energy dissipation using a unique two-photon absorption mechanism. Photon absorption by ground-state OCP (OCPO) generates a metastable intermediate (OCP1h{nu}) that either relaxes thermally or, upon absorption of a second photon within [~]1 s, converts to the active photoprotective state (OCPR). By integrating static and time-resolved crystallography, cryo-EM, computation, spectroscopy and biochemistry, we assign the structure of OCP1h{nu}, establish its functional relevance and capture structural snapshots along the OCPO[->]OCP1h{nu} and OCP1h{nu}[->]OCPR photochemical pathways. We elucidate the molecular mechanism of OCP, which serves as a unique biological circuit breaker protecting the photosynthetic machinery from high light flux.

biochemistry↗

bioRxiv2026

F1F0-ATP-synthase subunit b head-to-head interactions shape intracellular membranes in Escherichia coli

1Intracellular membrane (ICM) compartments in bacteria remain poorly understood. In Escherichia coli, ICMs form upon the overproduction of certain membrane proteins. Here, we investigate at the molecular level how overproduction of subunit b of the F1Fo-ATP synthase complex shapes ICMs. Through a combination of subunit b deletions, electron microscopy, and biochemical analyses, we demonstrate that ICMs network structuration is mediated by the C-terminal domain of subunit b. High-resolution cryo-electron tomography and molecular dynamics simulations reveal that this domain forms tetrameric assemblies, bridging membranes and maintaining a regular 26 nm spacing. Transcriptomic and proteomic analyses further show that the cell responds to ICMs formation by upregulating energy metabolism genes and the ESCRT-III homolog PspA, while downregulating ribosomal and translational machinery. These results uncover a novel mechanism by which the C-terminal domain of subunit b drives the structuring of intracellular membranes. Additionally, they highlight how E. coli adapts to membrane stress by overexpressing membrane-remodeling proteins, a response that shares similarities with intracellular membrane homeostasis mechanisms in photosynthetic bacteria and unicellular algae.

microbiology↗

bioRxiv2026

A dynamic displacement mechanism drives protein import into mitochondria

Most mitochondrial proteins are produced in the cytosol and imported through the translocase of the outer mitochondrial membrane (TOM) to reach their final destination. Although this protein entry gate has been structurally characterized, it remains unclear how precursor proteins are handed off from the cytosolic receptor domains to the translocation pore. Here we show that the cytosolic domain of Tom22--traditionally viewed as the central TOM receptor--acts not as a structured scaffold but as a largely disordered, flexible segment that plays an active role in precursor transfer. Atomic-level structural techniques and in vivo experiments identified a conserved short linear motif that forms a transient !-helical element within this disordered domain. By binding to the canonical precursor protein binding sites of the receptors Tom20 and Tom70, this critical -helical segment acts as a precursor protein displacement element (PPDE). This competitive interaction facilitates the release of preproteins directly above the import pore, and thereby drives translocation across the outer mitochondrial membrane. These findings reveal that flexibility, rather than rigid structure, underlies the central transfer step of mitochondrial outermembrane protein translocation. Our results point to a versatile mechanism for ligand displacement in chaperone, receptor, and transport systems that must balance selective binding with efficient release.

cell biology↗

bioRxiv2025

InterMap: Accelerated Detection of Interaction Fingerprints on Large-Scale Molecular Ensembles

MotivationMolecular dynamics is a key technique for exploring biomolecular systems at the atomic level. The rapid growth in accessible system sizes and timescales has intensified the need for efficient post-processing methods that extract meaningful insights from the resulting data. Interaction fingerprint (IFP) analyses are a valuable tool for elucidating key atomic interactions within molecular ensembles, yet current specialized software often struggle with extensive trajectories or complex systems. Here, we introduce InterMap, a Python package designed to accelerate IFP detection on large-scale molecular ensembles. ResultsBy actively exploiting k-d trees, InterMap efficiently handles the massive amount of distance calculations necessary to detect IFPs, particularly when dealing with intra-molecular interactions. The seamless integration with MDAnalysis ensures broad format compatibility and allows using SMARTS patterns for flexible interaction definitions. InterMap adopts a deeply compressed binary encoding to manage IFPs, which makes it very memory-friendly. Furthermore, convenient interactive visualizations are provided to enhance data interpretation through a locally hosted web-browser application. Benchmark results indicate that InterMap significantly outperforms existing tools for processing complex biomolecular systems, achieving up to a 99% reduction in both runtime and peak memory usage. AvailabilityInterMaps code and issue tracker are available at https://github.com/Delta-Research-Team/intermap.git, while documentation and tutorials can be found at https://delta-research-team.github.io/intermap/. Contactroy.gonzalez-aleman@inria.fr, yasaman.karami@inria.fr Supplementary informationSupplementary data are available at Nucleic Acid Research online.

bioinformatics↗

bioRxiv2025

Structures of the honeybee GABAA RDL receptor illuminate allosteric modulation

Insect GABAA receptors are critical insecticide targets, with all 21st-century commercial compounds acting through a single allosteric membrane site. Here we describe three ligand binding sites and the associated receptor conformations for the honeybee RDL receptor, combining cryo-EM, electrophysiology and molecular dynamics. First the conservation of the GABA site explains the absence of insect-selective orthosteric compounds. Second, the classical modulation site, occupied here by abamectin, exists in a closed-pore conformation contrasting with ivermectin-bound states in other receptors. Third, using the fungal-derived Chrodrimamin B, we resolve an unanticipated membrane modulation pocket structurally analogous yet pharmacologically opposite to a neurosteroid site in mammalian receptors. Structures also reveal the existence of an intersubunit, conformation-dependent, PIP2 lipid site. We foresee our results to be the starting point for investigations on the physiological modulation of insect GABAA receptors. The honeybee receptor structures may also foster the search for environmentally benign insecticides.

biophysics↗

bioRxiv2024

Asynchronous subunit transitions precede acetylcholine receptor activation

Rapid communication at synapses is facilitated by postsynaptic receptors, which convert a chemical signal into an electrical response. In the case of ligand-gated ion channels, agonist binding triggers rapid transition through a series of intermediate states leading to a transient open-pore conformation. These transitions are usually framed in terms of a mechanism where agonist binding and channel activation are separate events. Here, we collect cryo-EM images over a range of agonist concentrations to define structures of the muscle-type nicotinic acetylcholine receptor in unliganded, mono-liganded, and di-liganded states. We show that agonist binding to a single agonist site stabilizes an intermediate state where an entire principal agonist-binding subunit has transitioned to an active-like conformation, while the other unoccupied principal subunit remains inactive, albeit poised for activation. Binding of agonist to the second agonist site fully activates the remaining subunits leading to hydration of the ion pore. Uniting this cryo-EM derived intermediate structure with single-channel recordings leads to a model where individual acetylcholine receptor subunits asynchronously undergo conformational transitions, and thus a sequential activation mechanism that has implications for the entire superfamily of pentameric ligand-gated ion channels.

neuroscience↗

bioRxiv2024

Structural Determinants for Activity of the Antidepressant Vortioxetine at Human and Rodent 5-HT3 receptors

Vortioxetine (VTX) is a recent antidepressant that targets a variety of serotonin receptors. We investigate the drugs molecular mechanism of operation at serotonin 5-HT3 receptors (5-HT3R), which features two mysterious properties: VTX acts differently on rodent and human 5-HT3R; VTX appears to suppress any subsequent response to agonists. Using a combination of cryo-EM, electrophysiology, and molecular dynamics, we show that VTX stabilizes a resting inhibited state of the mouse 5-HT3R and an agonist bound-like state of the human 5-HT3R, in line with the functional profile of the drug. We report four human 5-HT3R structures and show that the human receptor transmembrane domain is intrinsically fragile. We also explain the lack of recovery after VTX administration via a membrane partition mechanism.

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↗

bioRxiv2020

Structure of HIV-1 gp41 with its membrane anchors targeted by neutralizing antibodies

The HIV-1 gp120/gp41 trimer undergoes a series of conformational changes in order to catalyze gp41-induced fusion of viral and cellular membranes. Here, we present the crystal structure of gp41 locked in a fusion intermediate state by an MPER-specific neutralizing antibody. The structure illustrates the conformational plasticity of the six membrane anchors arranged asymmetrically with the fusion peptides and the transmembrane regions pointing into different directions. Hinge regions located adjacent to the fusion peptide and the transmembrane region facilitate the conformational flexibility that allows high affinity binding of broadly neutralizing anti-MPER antibodies. Molecular dynamics simulation of the MPER Ab-induced gp41 conformation reveals the transition into the final post-fusion conformation with the central fusion peptides forming a hydrophobic core with flanking transmembrane regions. This, thus, suggests that MPER-specific broadly neutralizing antibodies can block final steps of refolding of the fusion peptide and the transmembrane region, which is required for completing membrane fusion.

microbiology↗

bioRxiv2020

The binding of palonosetron and other antiemetic drugs to the serotonin 5-HT3 receptor

Inaccurately perceived as niche drugs, antiemetics are key elements of cancer treatment alleviating the most dreaded side effect of chemotherapy. Serotonin 5-HT3 receptor antagonists are the most commonly prescribed class of drugs to control chemotherapy-induced nausea and vomiting (CINV). These antagonists have been clinically successful drugs since the 1980s, yet our understanding of how they operate at the molecular level has been hampered by the difficulty of obtaining structures of drug-receptor complexes. Here, we report the cryo-EM structure of the palonosetron-bound 5-HT3 receptor. We investigate the binding of palonosetron, granisetron, dolasetron, ondansetron, and cilansetron using molecular dynamics, covering the whole set of antagonists used in the clinical practice. The structural and computational results yield detailed atomic insight into the binding modes of the drugs. In light of our data, we establish a comprehensive framework underlying the inhibition mechanism by the -setron drug family.

neuroscience↗

bioRxiv2019

Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors

Coordinated conformational transitions in oligomeric enzymatic complexes modulate function in response to substrates and play a crucial role in enzyme inhibition and activation. ClpP protease is a tetradecameric complex that has emerged as a drug target against multiple pathogenic bacteria. During drug development efforts, the activation of different ClpPs by inhibitors was independently reported, but so far, no rationale for inhibitor-induced activation has been proposed. Using an integrated approach that included X-ray crystallography, solid-and solution-state NMR, MD simulations and ITC we show that the proteasome-inhibitor bortezomib binds to the ClpP active site serine mimicking a peptide substrate and induces the concerted allosteric activation of the complex. The bortezomib activated conformation also displays a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric mechanism where substrate binding to a single subunit locks ClpP into an active conformation optimized for chaperone association as well as protein processive degradation.

biochemistry↗

bioRxiv2018

Dynamics and interactions of ADP/ATP transporter AAC3 in DPC detergent are not functionally relevant

A recent study1 used solution-state NMR spectroscopy to examine the interactions and dynamics of the yeast mitochondrial inner-membrane ADP/ATP carrier, yAAC3. Crystal structures of different AACs, including yAAC3, in a conformation locked with a strong inhibitor (CATR) had been determined before. This putative \"c-state\"2,3 is believed to represent one extreme conformation of an alternating access mechanism, which involves a further and yet elusive second state termed \"m-state\". Characterizing the dynamics between these states is of paramount importance to understand the transport mechanism. The authors refolded yAAC3 from inclusion bodies in the detergent dodecylphosphocholine (DPC), and observed micro-to-millisecond (s-ms) motion in part of yAAC3 using CPMG NMR experiments. The authors propose that this asymmetrically distributed dynamics, involving residues located in thr ...

biophysics↗