Enhancing the Assembly Properties of Bottom-Up Coarse-Grained Phospholipids.

Abstract

A plethora of key biological events occur at the cellular membrane where the large spatiotemporal scales necessitate dimensionality reduction or coarse-graining approaches over conventional all-atom molecular dynamics simulation. Constructing coarse-grained descriptions of membranes systematically from statistical mechanical principles has largely remained challenging due to the necessity of capturing amphipathic self-assembling behavior in coarse-grained models. We show that bottom-up coarse-grained lipid models can possess metastable morphological behavior and that this potential metastability has ramifications for accurate development and training. We in turn develop a training algorithm which evades metastability issues by linking model training to self-assembling behavior, and demonstrate its robustness via construction of solvent-free coarse-grained models of various phospholipid membranes, including lipid species such as phosphatidylcholines, phosphatidylserines, sphingolipids, and cholesterol. The resulting coarse-grained lipid models are orders of magnitude faster than their atomistic counterparts while retaining structural fidelity and constitute a promising direction for the development of coarse-grained models of realistic cell membranes.