Shocker - a molecular dynamics protocol and tool for accelerating and analyzing the effects of osmotic shocks

Abstract

AbstractThe process of osmosis, a fundamental phenomenon in life, drives water through a semi-permeable membrane in response to a solute concentration gradient across this membrane. In vitro, osmotic shocks are often used to drive shape changes in lipid vesicles, for instance, to study fission events in the context of artificial cells. While experimental techniques provide a macroscopic picture of large-scale membrane remodeling processes, molecular dynamics (MD) simulations are a powerful tool to study membrane deformations at the molecular level. However, simulating an osmotic shock is a time-consuming process due to the slow water diffusion across the membrane, making it practically impossible to examine its effects in classic MD simulations. In this paper, we present Shocker, a Python-based MD tool for simulating the effects of an osmotic shock by selecting and relocating water particles across a membrane over the course of several pumping cycles. Although this method is primarily aimed at efficiently simulating volume changes of vesicles it can handle membrane tubes and double bilayer systems as well. Additionally, Shocker is force field independent and compatible with both coarse-grained and all-atom systems. We demonstrate that our tool is applicable to simulate both hypertonic and hypotonic osmotic shocks for a range of vesicular and bilamellar setups, including complex multi-component systems containing membrane proteins or crowded internal solutions.