The synthesis by solid-phase methodologies of peptides belonging to structural and non-structural proteins of GB virus C as well as its N-alpha-acylation with myristate and palmitate fatty acids is described. To explore the peptide-lipid interactions we have used liposomes composed of dipalmitoylphosphatidylcholine as model membranes and complementary spectroscopic and calorimetric techniques. Our results show that structural and more clearly the structural lipophilic peptide sequences incorporated into lipid bilayers perturb the packing of lipids and affect their thermotropic properties, more than the non-structural selected sequence. However, the binding of the synthetic sequences to lipid membranes occurred without any restructuration of the peptides.