BPS2026 – Lipid droplet and membrane biogenesis in silico

Lipid droplets (LDs) are organelles regulating lipid storage and metabolism in cells. LD biogenesis takes place mostly in the endoplasmic reticulum (ER), and starts with the synthesis of neutral lipids, such as triglycerides. When the concentration of neutral lipids reaches a certain threshold, oil droplets form by phase-separation, yielding a lens-shaped nascent lipid droplet—a process known as nucleation. As more neutral lipids are synthesized, the lens grows and eventually buds out of the ER membrane, generally toward the cytosol, at sites marked by a specific protein named seipin. Several open questions remain regarding the mechanism of LD budding, because the initial steps of LD biogenesis are extremely difficult to observe experimentally. Notably, the roles of ER topology, leaflet asymmetry, and membrane composition in the budding mechanism are substantially unknown. Here, we develop a new methodology, coined POP-MD, to simulate changes in size, composition, and asymmetry in lipid membranes of arbitrary shape and chemical complexity. In POP-MD, molecular dynamics simulations are performed out of equilibrium, by analogy with real life experiments. We then use POP-MD to generate lipid droplets in membranes mimicking the topology and composition of the tubular ER, and explore possible mechanisms of LD budding. Simulations show that the LD budding mechanism depends on the specific conditions imposed on the system, and allow predictions on the localization of phospholipid and triglyceride synthesis, the role of seipin, and the stability of the ER-LD connection. Our method pushes the limit of biological simulations producing, for the first time, a dynamic picture of organelle biogenesis with nanosecond time resolution and molecular-level detail.