In this study, we observed the structural and energetic stability of a polypeptide nanosheet formed by a polypeptide skeleton of six alanines (ALA) or leucines (LEU) and a polar head composed of aspartic acid (ASP), lysine (LYS) or arginine (ARG). The six membrane structures A6D, A6K, A6R, L6D, L6K, and L6R were subjected to molecular dynamics simulations in an ionic liquid formed by the cholinium–glycine pair [CHO][GLY]. Our results show how the hydrogen bonds between the polypeptides and the ionic liquid are structured, the energetic behavior of the nanosheet, mobility of the IL, surface topology of the membrane and the stiffness of the structure when the extraction of a polypeptide from the macro structure is carried out. Different structural combinations were considered to verify the difference due to the electrostatic behavior in the systems. Our analysis aims to contribute information that can increase the use of these organic and biodegradable materials in other environments.