Nano-architectures self-assembled from rationally designed peptides and proteins are essential components of molecular robots. By engineering self-assembly based on peptide secondary structures, protein–ligand interactions, and protein–protein interactions, various nanostructures can be constructed, including fibers, tubes, rings, and capsules. For these nano-architectures to function as elements of molecular robots, they should interact with liposomes—the compartments of molecular robots—and perturb them in response to stimuli. Studies have investigated morphological changes in liposomes accompanying structural changes in peptide assemblies in response to stimuli, as well as substance transfer and signal transduction across the liposome membrane. This chapter outlines recent studies on liposome deformation and substance transport across membranes based on interactions between peptide assemblies and lipid membranes.