Biology subjects

Monticelli, L.

Publications and source records attributed to Monticelli, L..

6 recordsLinked to original sources

bioRxiv2026

Lipid droplet shape and tendency towards budding: insight from theory and molecular simulations

Lipid droplets (LDs) are cellular organelles responsible for lipid storage and metabolism. The mechanism of biogenesis of LDs involves phase separation of neutral lipids from the surrounding phospholipids, which generates oil lenses embedded in lipid bilayers, also known as nascent LDs. As nascent LDs grow, at some point they bud out of the bilayer, forming nearly spherical droplets. Nascent LDs have different propensity to bud, and it has been proposed that their shape provides information on such propensity; however, LD shape is difficult to determine experimentally. Here we studied the shape of lipid droplets using MD simulations at the coarse-grained level, and compared it to the predictions by an established theory. Our general system setup features an oil lens embedded into a flat, periodic bilayer. We found that the shape of simulated nascent LDs resembles a spherical cap (i.e., it has constant curvature over most of the surface), in excellent agreement with the theory, already for very small droplet sizes. The aspect ratio (height/radius) of nascent LDs increases with increasing LD volume, increasing membrane softness, and increasing surface tension between oil and water, also in agreement with theoretical predictions; however, it remains lower than 1 (i.e., the ratio for a sphere) for LDs of up to 40 nm in diameter. Fitting the simulated LD shapes with a theoretical shape equation suggests that a non-zero surface tension is present in both the monolayer and in the bilayer region. The existence of a relatively high surface tension in the bilayer region is confirmed by local stress calculations, and indicates that the periodic system setup does not reproduce the properties of nascent LDs in the endoplasmic reticulum, where the bilayer tension is two orders of magnitude lower. However, the simulations provide a microscopic view into the properties of droplet embedded vesicles.

biophysics↗

bioRxiv2025

Post-translational acylation drives folding and activity of the CyaA bacterial toxin.

Post-translational modifications critically shape protein conformation and function, yet how they regulate bacterial toxins remains elusive. The adenylate cyclase (CyaA) toxin is a major virulence factor of Bordetella pertussis, the causative agent of whooping cough. CyaA is produced as an inactive precursor, proCyaA, which is activated by acylation of two lysine residues within the bacterium. Once acylated and secreted, CyaA invades innate immune cells and disrupts their phagocytic functions. High-resolution structural characterization of CyaA has remained elusive due to its size, multi-domain organization, flexibility, and aggregation propensity. Here, we overcome these challenges and generate the first structural ensembles of both non-acylated and acylated CyaA in solution by combining experimental data with integrative modeling. Coarse-grained molecular dynamics simulations reveal that acylation is critical to stabilize the native fold and to favorably orient CyaA on the target membrane. Overall, our findings reveal how post-translational acylation triggers native folding and provide mechanistic insights into the early steps of host cell intoxication.

biophysics↗

bioRxiv2025

Ist2, a protein involved in phosphatidylserine transport, is an ER lipid scramblase

Lipid scramblases allow passive flip-flop of phospholipids between bilayer leaflets, thereby promoting membrane symmetry. At the endoplasmic reticulum (ER), where phospholipid synthesis is restricted to one of the two leaflets, scramblase activity should be essential for equilibrated membrane growth. However, phospholipid scramblases at the ER are poorly understood. The yeast protein Ist2 contains an ER domain and a cytosolic tail that binds the plasma membrane (PM) and participates in the transfer of phosphatidylserine (PS). Here, we show both in vitro and in silico that the ER- domain of Ist2, which bears homology to the TMEM16 proteins, possesses a lipid scramblase activity. Ist2 activity is not regulated by Ca2+, in contrast to TMEM16 proteins, but is affected by the lipid composition of the bilayer used in simulations. In cells, we do not find a strong impact of the scramblase domain of Ist2 in on PS distribution; however, its over-expression or deletion affects processes at the ER such as vesicular transport, lipid droplet biogenesis and general phospholipid transport, with a specific contribution of residues important for lipid scrambling. Our study therefore identifies the first dedicated phospholipid scramblase in yeast and demonstrates that membrane asymmetry can impact diverse membrane-remodeling processes at the ER.

cell biology↗

bioRxiv2024

GoMartini 3: From large conformational changes in proteins to environmental bias corrections

Coarse-grained modeling has become an important tool to supplement experimental measurements, allowing access to spatio-temporal scales beyond all-atom based approaches. The G[o]Martini model combines structure- and physics-based coarse-grained approaches, balancing computational efficiency and accurate representation of protein dynamics with the capabilities of studying proteins in different biological environments. This paper introduces an enhanced G[o]Martini model, which combines a virtual-site implementation of G[o] models with Martini 3. The implementation has been extensively tested by the community since the release of the new version of Martini. This work demonstrates the capabilities of the model in diverse case studies, ranging from protein-membrane binding to protein-ligand interactions and AFM force profile calculations. The model is also versatile, as it can address recent inaccuracies reported in the Martini protein model. Lastly, the paper discusses the advantages, limitations, and future perspectives of the Martini 3 protein model and its combination with G[o] models.

biophysics↗

bioRxiv2023

Birth of an organelle: molecular mechanism of lipid droplet biogenesis

Lipid droplets (LDs) are cellular organelles regulating energy and lipid metabolism. Generated in the endoplasmic reticulum (ER) by phase separation of neutral lipids (e.g., triglycerides), nascent LDs resemble lens-shaped blisters, grow into spherical droplets, and eventually emerge from the ER membrane, generally towards the cytosol - a process known as budding. Images of both nascent and mature LDs are available, but the mechanism of biogenesis has never been observed experimentally. Here we identify the mechanism of the initial steps in LD biogenesis using computer simulations at the molecular level, emulating LD growth in ER-mimicking membranes. We find that LDs bud towards the cytosol only when sufficient asymmetry is generated between the two membrane leaflets: the budding transition is independent of membrane morphology, lipid composition, and LD size. Seipin, a protein essential for correct LD biogenesis, is per se not sufficient to promote budding, but it stabilizes LD-ER contact sites. Localization of triglyceride synthesis in the proximity of seipin is necessary to avoid nucleation of multiple LDs - a possible cause of aberrant phenotypes. In contrast, localization of phospholipid synthesis has no effect on the mechanism of budding. Our new methodology paves the way to simulations of organelle and cell biogenesis.

biophysics↗

bioRxiv2022

Coarse-graining made easy with the MArtini Database Server

The MArtini Database (MAD - www.mad.ibcp.fr) is a web server designed for the sharing structures and topologies of molecules parameterized with the Martini coarse-grained (CG) force field. MAD can also convert atomistic structures into CG structures and prepare complex systems (including proteins, lipids etc.) for molecular dynamics (MD) simulations at the CG level. It is dedicated to the generation of input files for Martini 3, the most recent version of this popular CG force field. Specifically, the MAD server currently includes tools to submit or retrieve CG models of a wide range of molecules (lipids, carbohydrates, nanoparticles, etc.), transform atomistic protein structures into CG structures and topologies, with fine control on the process and assemble biomolecules into large systems and deliver all files necessary to start simulations in the GROMACS MD engine.

biophysics↗