Biology subjects

Allolio, C.

Publications and source records attributed to Allolio, C..

9 recordsLinked to original sources

bioRxiv2026

Direct Membrane Penetration of Oligoarginines by Fluorescence and Cryo-electron Microscopy Combined with Molecular Simulations

Arginine-rich peptides are short amino acid chains capable of spontaneously crossing cellular membranes, with great potential for drug or other cargo delivery. Yet, the mechanisms underlying their cellular penetration are not fully understood. Here, we investigate the modes of action of nonaarginine (R9) across membranes of increasing compositional and biological complexity. We combine computational, fluorescence microscopy, and cryo-EM approaches to both visualize the membrane structural changes arising from peptide-lipid interactions and provide a molecular rationale for the observed effects. In large unilamellar vesicles, R9 binds preferentially to anionic and PE-rich membranes, induces lipid reorganization, and drives pronounced remodelling, including budding, bifurcations, and time-dependent formation of multilamellar stacks. In cell-derived extracellular vesicles, R9-induced remodelling is largely confined to bilamellar bifurcations. In live cells, fluorescent R9 forms surface puncta that precede cytosolic entry. Correlative cryo-fluorescence and electron tomography reveals that these puncta correspond to strongly folded, multilamellar membrane structures. We propose that these seemingly contrasting observations can be reconciled within a single R9 mechanism of action, involving membrane folding and stacking, where the different observed morphologies arise from the size of the accessible membrane reservoir.

biophysics↗

bioRxiv2025

Molecular Grammar of Microtubule-WettingCondensates

Microtubule condensate interactions are fundamental for cell division, vesicle transport and cellular locomotion. Accordingly, they represent a large number of attractive drug targets. Due to the size of microtubuli and the slow timescale of condensate structural relaxation, there has not been a systematic investigation at the molecular level as to what binding patterns (molecular grammar) enable condensate binding to microtubuli. We provide a protocol that is able to predict whether any given disordered protein sequence will bind to microtubuli. This protocol is suitable for compound screening. Our pattern analysis allows us to establish two categories of strongly interacting subsequences that enable binding to microtubuli: positively charged hydrophobic clusters and alternating charge sequences. Their overall optimal balance is analyzed and preferential regions of interaction on microtubuli are identified and validated with known experimental results. Our results enable rapid prototyping of proteins that target the microtubule surface, i.e. they predict whether unstructured proteins will wet the microtubule interface.

biophysics↗

bioRxiv2025

From Molecular Insight to Mesoscale MembraneRemodeling: Curvature Generation byArginine-Rich Cell-Penetrating Peptides

The enhanced cell penetration ability of arginine-rich peptides, such as nonaarginine (R9), compared to their lysine-rich counterparts remains incompletely understood. Atomistic simulations reveal that R9 binds significantly more strongly ({approx} 20 kJ/mol) and penetrates deeper into anionic lipid headgroup region than its lysine equivalent. This enhanced interaction translates into a stronger induction of negative membrane curvature by R9. We combine these data to construct a model of peptide binding and curvature induction in fusogenic lipid mixtures and employ a multiscale simulation approach, combining atomistic molecular dynamics (MD) with mesoscopic Monte Carlo (MC) simulations, to dissect the molecular basis and morphological consequences of arginine specificity. The results show that stable membrane invaginations, as observed in studies of cell penetration, require excess membrane and are stable only for R9 (outside of the domain of stability of the Helfrich stomatocyte). By analyzing lipid and protein sorting coupled to the membrane structure, we explain the interplay of Gaussian and mean curvature in providing a mechanistic basis for the initial membrane deformation events potentially involved in Arginine Magic cell entry pathways.

biophysics↗

bioRxiv2024

Stress-mediated growth determines E. coli division site morphogenesis

In order to proliferate, bacteria must remodel their cell wall at the division site. The division process is driven by the enzymatic activity of peptidoglycan (PG) synthases and hydrolases around the constricting Z-ring. PG remodelling is reg-ulated by de-and re-crosslinking enzymes, and the directing constrictive force of the Z-ring. We introduce a model that is able to reproduce correctly the shape of the division site during the constriction and septation phase of E. coli. The model represents mechanochemical coupling within the mathematical framework of morphoelasticity. It contains only two parameters, associated with volumet-ric growth and PG remodelling, that are coupled to the mechanical stress in the bacterial wall. Different morphologies, corresponding either to mutant or wild type cells were recovered as a function of the remodeling parameter. In addition, a plausible range for the cell stiffness and turgor pressure was determined by comparing numerical simulations with bacterial cell lysis data.

biophysics↗

bioRxiv2024

Pore formation in complex biological membranes: torn between evolutionary needs

The primary function of biological membranes is to enable compartmentalization among cells and organelles. Loss of integrity by the formation of membrane pores would trigger uncontrolled depolarization or influx of toxic compounds, posing a fatal thread to living cells. How the lipid complexity of biological membranes enables mechanical stability against pore formation while simultaneously allowing ongoing membrane remodeling is largely enigmatic. We performed molecular dynamics simulations of eight complex lipid membranes including the plasma membrane and membranes of the organelles ER, Golgi, lysosome, and mitochondrion. To quantify the mechanical stability of these membranes, we computed the free energies for nucleating a transmembrane pore as well as the line tension along the rim of open pores. Our simulations reveal that complex biological membranes are overall remarkably stable, however with the plasma membrane standing out as exceptionally stable, which aligns with its crucial role as a protective layer. We observe that sterol content is the main regulator for biomembrane stability, and that lateral sorting among lipid mixtures influences the energetics of membrane pores. A comparison of 25 model membranes with varying sterol content, tail length, tail saturation, and head group type shows that the pore nucleation free energy is mostly associated with the lipid tilt modulus, whereas the line tension along the pore rim is determined by the lipid intrinsic curvature. Together, our study provides an atomistic and energetic view on the role of lipid complexity on biomembrane stability. Significance statementBiomembranes have evolved to fulfill seemingly conflicting requirements. Membranes form a protective layer against bacterial or viral infection and against external mechanical and toxic stress, thus requiring mechanical stability. However, membranes are furthermore involved in ongoing remodeling for homeostasis, signaling, trafficking, and morphogenesis, necessitating a high degree of plasticity. How the chemical diversity of membranes, comprising hundreds of lipid species, contributes to enable both stability and plasticity is not well understood. We used molecular simulations and free energy calculations of pore formation in complex biomembranes to reveal how mechanical and geometric properties of lipids as well as lateral lipid sorting control the integrity of complex membranes.

biophysics↗

bioRxiv2023

OrganL: Dynamic Triangulation of Biomembranes using Curved Elements

We describe a method for simulating biomembranes of arbitrary shape. In contrast to other dynamically triangulated surface (DTS) algorithms, our method provides a rich, quasi tangent-continuous, yet local description of the surface. We use curved Nagata triangles, which we generalize to cubic order to achieve the requisite flexibility. The resulting interpolation can be constructed locally without iterations. This allows us to provide a parallelized and fine-tuned Monte Carlo implementation. As a first example of the potential benefits of the enhanced description, our method supports inhomogeneous lipid properties as well as lipid mixing. It also supports restraints and constraints of various types and is constructed to be as easily extensible as possible. We validate the approach by testing its numerical accuracy, followed by reproducing the known Helfrich solutions for shapes with rotational symmetry. Finally, we present some example applications, including curvature-driven demixing and stylized effects of proteins. Input files for these examples, as well as the implementation itself, are freely available for researchers under the name OrganL. O_TEXTBOXOur method provides a straightforward way to simulate any biomembrane geometry. It overcomes some of the limitations of previous dynamically triangulated surface (DTS) Monte Carlo schemes by providing a surface that contains an interpolant which allows to assign meaningful functions of curvature to almost every point of the discretization, yet keeps much of the simplicity of the common DTS schemes by not requiring any nonlocal information or iterations for its construction. Our tool is easily extensible and facilitates the simulation of complex lipid and protein compositions on membrane surfaces at any scale. C_TEXTBOX

biophysics↗

bioRxiv2023

Mitochondrial Membranes: Model Lipid Compositions, Material Properties and the Changing Curvature of Cardiolipin

Mammalian and Drosophila Melanogaster model mitochondrial membrane compositions are constructed from experimental lipidomics data. Simplified compositions for inner and outer mitochondrial membranes are provided, including an asymmetric inner mitochondrial membrane. We performed atomistic molecular dynamics simulations of these membranes and computed their material properties. When comparing these properties to those obtained by extrapolation from their constituting lipids, we find good overall agreement. Finally, we analyzed the curvature effect of cardiolipin, considering ion concentration effects, oxidation and pH. We draw the conclusion that cardiolipin negative curvature is most likely due to counterion effects, such as cation adsorption, in particular of H3O+. This oft-neglected effect might account for the puzzling behavior of this lipid. SIGNIFICANCEMitochondrial membranes are of fundamental interest to the pathogenesis of neurodegenerative diseases. The biophysics of mitochondrial membranes can be expected to profoundly influence both the electron transport chain and larger-scale mitochondrial morphology. We provide model mitochondrial membrane compositions and examine their mechanic properties. Reconstructing these properties from their constituent lipids, we facilitate the creation of mesoscopic models. Cardiolipin, as the key mitochondrial lipid is given special attention. We find that its mechanical properties, in particular its curvature, are not constant, but highly dependent on specific ion effects, concentration and oxidation state.

biophysics↗

bioRxiv2021

Cell wall synthesis and remodeling dynamics determine bacterial division site architecture and cell shape

The bacterial division apparatus builds daughter cell poles by catalyzing the synthesis and remodeling of the septal peptidoglycan (sPG) cell wall. Understanding of this essential process has been limited by the lack of native three-dimensional visualization of developing septa. Here, we used state-of-the-art cryogenic electron tomography (cryo-ET) and fluorescence microscopy to understand the division site architecture and sPG biogenesis dynamics of the Gram-negative bacterium Escherichia coli. Our results with mutant cells altered in the regulation of sPG biogenesis revealed a striking and unexpected similarity between the architecture of E. coli septa with those from Gram-positive bacteria, suggesting a conserved morphogenic mechanism. Furthermore, we found that the cell elongation and division machineries are in competition and that their relative activities determine the shape of cell constrictions and the poles they form. Overall, our results highlight how the activity of the division system can be modulated to generate the diverse array of morphologies observed in the bacterial domain. HighlightsO_LIThe division site architecture of E. coli can be modulated to resemble that of diverse bacteria. C_LIO_LICell wall degradation at the division site activates septal cell wall synthesis. C_LIO_LIAssembly of the cytoskeletal ring at the division site is modulated by cell wall remodeling. C_LIO_LIBalance between the activities of the elongation and division systems modulates cell shape. C_LI

microbiology↗

bioRxiv2020

Calcium ions promote membrane fusion by forming negative-curvature inducing clusters on specific anionic lipids

Vesicles enriched in certain negatively charged lipids, such as phosphatidylserine and PIP2, are known to undergo fusion in the presence of calcium ions without assistance from protein assemblies. Other lipids do not exhibit this propensity, even if they are negatively charged. Using our recently developed methodology, we extract elastic properties of a representative set of lipids. This allows us to trace the origin of lipid-calcium selectivity in membrane fusion to the formation of lipid clusters with long-range correlations that induce negative curvature on the membrane surface. Furthermore, the clusters generate lateral tension in the headgroup region at the membrane surface, concomitantly increasing its Gaussian bending modulus. Finally, calcium binding also reduces the orientational polarization of water around the membrane headgroups, potentially reducing the hydration force acting between membranes. Binding calcium only weakly increases membrane bending rigidity and tilt moduli, in agreement with experiments. We show how the combined effects of calcium binding to membranes lower the barriers along the fusion pathway that lead to the formation of the fusion stalk as well as the fusion pore.

biophysics↗