The Vesicle Builder - A Membrane Packing Algorithm for the CELLmicrocosmos MembraneEditor

Abstract

For a long time, the major focus of membrane simulations was laid on rectangular membrane patches based on the fluid mosaic model. Because of the computational performance of today's computer hardware, it is now possible to generate and simulate larger structures, such as vesicles or micelles. Yet, there are no approaches available to generate these partly complex structures in a convenient and interactive way using WYSIWYG methods and exporting it to PDB format. The CELLmicrocosmos 2.2 MembraneEditor was originally developed for the interactive computation of heterogeneous rectangular membrane patches, solving 2.5D packing problems. Now, its packing capabilities were extended into the third dimension by introducing the Vesicle Builder which is optimized for the computation of vesicular mono- or bilayer membranes. The shape computation is based on an ellipsoid formula enabling the generation of vesicles featuring different lipid compositions, shapes and sizes. More complex shapes can be generated by combining different shapes. Moreover, extended shape customization is possible by modifying and extending the algorithm. Three application cases are discussed: 1) Different potential vesicular configurations including wavy, ellipsoid, enclosing and modular structures are modelled and shortly discussed; 2) To evaluate the compatibility of the Vesicle Builder with simulation tools, a three-component vesicle was modelled and successfully simulated. 3) To show the capability to generate large structures, a vesicle with a radius of 370 Å was generated, consisting of approx. 50,000 lipids and 2 million atoms, respectively. The MembraneEditor as well as the Vesicle Builder plugin can be downloaded from https://Cm2.CELLmicrocosmos.org